Starting phenix.real_space_refine on Thu Jul 2 04:09:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.cif" model { file = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2026/7u9o_26402.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 25 5.16 5 C 4196 2.51 5 N 1088 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 6563 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2078 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 15, 'TRANS': 248} Chain breaks: 2 Chain: "B" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1472 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 9 Chain: "H" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1519 Classifications: {'peptide': 199} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 185} Chain breaks: 4 Chain: "L" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1452 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain breaks: 2 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.58, per 1000 atoms: 0.24 Number of scatterers: 6563 At special positions: 0 Unit cell: (94.284, 105.633, 142.299, 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 25 16.00 O 1254 8.00 N 1088 7.00 C 4196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " 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 234 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 351.3 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 5.3% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.081A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.808A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.046A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.825A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.904A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.773A 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 removed outlier: 3.737A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.674A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.656A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.525A pdb=" N GLU H 99 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.223A pdb=" N VAL H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.822A pdb=" N GLY H 150 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL H 193 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU H 152 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER H 191 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS H 154 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU H 189 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.900A pdb=" N VAL H 209 " --> pdb=" O TRP H 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.332A pdb=" N TYR H 205 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.650A pdb=" N TYR L 32 " --> pdb=" O ARG L 91 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.591A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.661A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU L 176 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER L 163 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 146 through 148 175 hydrogen bonds defined for protein. 405 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: 1.02 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2066 1.34 - 1.47: 1784 1.47 - 1.59: 2841 1.59 - 1.72: 0 1.72 - 1.85: 29 Bond restraints: 6720 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.28e+00 bond pdb=" CB ARG A 509 " pdb=" CG ARG A 509 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.93e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" N THR L 98 " pdb=" CA THR L 98 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.17e+00 ... (remaining 6715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 8700 1.94 - 3.88: 368 3.88 - 5.82: 44 5.82 - 7.76: 18 7.76 - 9.69: 3 Bond angle restraints: 9133 Sorted by residual: angle pdb=" N GLN L 27 " pdb=" CA GLN L 27 " pdb=" C GLN L 27 " ideal model delta sigma weight residual 110.80 120.49 -9.69 2.13e+00 2.20e-01 2.07e+01 angle pdb=" N GLY A 566 " pdb=" CA GLY A 566 " pdb=" C GLY A 566 " ideal model delta sigma weight residual 113.18 122.83 -9.65 2.37e+00 1.78e-01 1.66e+01 angle pdb=" C ALA H 214 " pdb=" N THR H 215 " pdb=" CA THR H 215 " ideal model delta sigma weight residual 124.21 128.84 -4.63 1.21e+00 6.83e-01 1.47e+01 angle pdb=" CA TRP L 94 " pdb=" C TRP L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 118.44 124.23 -5.79 1.59e+00 3.96e-01 1.33e+01 angle pdb=" C SER L 26 " pdb=" N GLN L 27 " pdb=" CA GLN L 27 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 ... (remaining 9128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 3731 15.35 - 30.69: 165 30.69 - 46.04: 42 46.04 - 61.39: 4 61.39 - 76.73: 6 Dihedral angle restraints: 3948 sinusoidal: 1552 harmonic: 2396 Sorted by residual: dihedral pdb=" CA TYR L 141 " pdb=" C TYR L 141 " pdb=" N PRO L 142 " pdb=" CA PRO L 142 " ideal model delta harmonic sigma weight residual 180.00 122.54 57.46 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA SER L 26 " pdb=" C SER L 26 " pdb=" N GLN L 27 " pdb=" CA GLN L 27 " ideal model delta harmonic sigma weight residual -180.00 -145.65 -34.35 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLN L 27 " pdb=" C GLN L 27 " pdb=" N SER L 28 " pdb=" CA SER L 28 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 3945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 694 0.053 - 0.105: 241 0.105 - 0.158: 70 0.158 - 0.211: 15 0.211 - 0.263: 3 Chirality restraints: 1023 Sorted by residual: chirality pdb=" CB THR L 98 " pdb=" CA THR L 98 " pdb=" OG1 THR L 98 " pdb=" CG2 THR L 98 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TRP L 94 " pdb=" N TRP L 94 " pdb=" C TRP L 94 " pdb=" CB TRP L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB THR H 106 " pdb=" CA THR H 106 " pdb=" OG1 THR H 106 " pdb=" CG2 THR H 106 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1020 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 141 " 0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO L 142 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO L 142 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 142 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.021 2.00e-02 2.50e+03 2.22e-02 8.61e+00 pdb=" CG PHE A 347 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU L 79 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO L 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.033 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2046 2.84 - 3.36: 4905 3.36 - 3.87: 9794 3.87 - 4.39: 10568 4.39 - 4.90: 19739 Nonbonded interactions: 47052 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.330 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.330 3.040 nonbonded pdb=" OG SER A 555 " pdb=" OD1 ASP A 586 " model vdw 2.364 3.040 nonbonded pdb=" O ILE L 107 " pdb=" OH TYR L 141 " model vdw 2.390 3.040 nonbonded pdb=" NH1 ARG L 109 " pdb=" O ASP L 171 " model vdw 2.399 3.120 ... (remaining 47047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.007 0.073 6733 Z= 0.301 Angle : 0.932 9.694 9162 Z= 0.509 Chirality : 0.060 0.263 1023 Planarity : 0.009 0.081 1164 Dihedral : 9.993 76.733 2374 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 0.28 % Allowed : 2.34 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.13 % 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: -4.13 (0.26), residues: 787 helix: -4.44 (0.42), residues: 32 sheet: -2.18 (0.29), residues: 282 loop : -3.10 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 54 TYR 0.037 0.004 TYR A 495 PHE 0.050 0.003 PHE A 347 TRP 0.034 0.003 TRP H 114 HIS 0.020 0.004 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.30 ( 6720) covalent geometry : angle 0.92126 / 0.51 ( 9133) SS BOND : bond 0.00714 / 0.42 ( 10) SS BOND : angle 2.08299 / 1.21 ( 20) hydrogen bonds : bond 0.27128 / 17.94 ( 164) hydrogen bonds : angle 10.35878 / 6.85 ( 405) link_NAG-ASN : bond 0.00439 / 0.21 ( 3) link_NAG-ASN : angle 3.67077 / 2.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.5698 (p) cc_final: 0.5349 (p) REVERT: A 574 ASP cc_start: 0.8199 (p0) cc_final: 0.7963 (p0) REVERT: A 584 ILE cc_start: 0.8811 (mm) cc_final: 0.8596 (mp) REVERT: A 586 ASP cc_start: 0.7872 (m-30) cc_final: 0.7643 (t0) REVERT: B 41 LYS cc_start: 0.8265 (mtpt) cc_final: 0.6500 (tptt) REVERT: B 134 GLN cc_start: 0.6283 (tp40) cc_final: 0.5897 (pm20) REVERT: B 202 LYS cc_start: 0.8288 (mttp) cc_final: 0.7829 (mttm) REVERT: B 278 LYS cc_start: 0.8149 (tttt) cc_final: 0.6933 (mttt) REVERT: H 220 ARG cc_start: 0.7815 (tpt170) cc_final: 0.7604 (tpp-160) outliers start: 2 outliers final: 1 residues processed: 175 average time/residue: 0.0943 time to fit residues: 21.1066 Evaluate side-chains 114 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 282 ASN H 208 ASN L 6 GLN L 90 GLN L 167 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107114 restraints weight = 8166.739| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.50 r_work: 0.3122 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6733 Z= 0.114 Angle : 0.631 12.451 9162 Z= 0.319 Chirality : 0.048 0.344 1023 Planarity : 0.006 0.068 1164 Dihedral : 5.623 54.823 888 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.93 % Allowed : 5.92 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -3.34 (0.27), residues: 787 helix: -4.00 (0.44), residues: 26 sheet: -1.35 (0.32), residues: 262 loop : -2.76 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.013 0.001 TYR L 174 PHE 0.014 0.001 PHE B 220 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 6720) covalent geometry : angle 0.62934 / 0.32 ( 9133) SS BOND : bond 0.00633 / 0.43 ( 10) SS BOND : angle 0.77491 / 0.54 ( 20) hydrogen bonds : bond 0.03331 / 2.14 ( 164) hydrogen bonds : angle 6.70104 / 4.41 ( 405) link_NAG-ASN : bond 0.00164 / 0.08 ( 3) link_NAG-ASN : angle 1.41213 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.6675 (p) cc_final: 0.6253 (p) REVERT: A 525 CYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6929 (m) REVERT: B 41 LYS cc_start: 0.8114 (mtpt) cc_final: 0.6364 (tptt) REVERT: B 134 GLN cc_start: 0.6142 (tp40) cc_final: 0.5692 (pm20) REVERT: B 237 ARG cc_start: 0.7718 (mtm180) cc_final: 0.6497 (ttm-80) REVERT: H 116 GLN cc_start: 0.8569 (pm20) cc_final: 0.8105 (pm20) REVERT: H 220 ARG cc_start: 0.7900 (tpt170) cc_final: 0.7544 (tpp-160) REVERT: L 11 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8073 (tt) REVERT: L 177 SER cc_start: 0.8907 (p) cc_final: 0.8652 (m) outliers start: 14 outliers final: 7 residues processed: 134 average time/residue: 0.0894 time to fit residues: 15.8346 Evaluate side-chains 117 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 186 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN L 6 GLN L 125 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103944 restraints weight = 8292.230| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.48 r_work: 0.2988 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6733 Z= 0.219 Angle : 0.689 8.948 9162 Z= 0.352 Chirality : 0.050 0.394 1023 Planarity : 0.006 0.070 1164 Dihedral : 5.616 54.566 888 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.75 % Allowed : 7.44 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.98 (0.28), residues: 787 helix: -3.28 (0.62), residues: 26 sheet: -1.10 (0.33), residues: 258 loop : -2.53 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.025 0.002 TYR A 495 PHE 0.019 0.002 PHE A 347 TRP 0.017 0.002 TRP H 114 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 ( 6720) covalent geometry : angle 0.68540 / 0.35 ( 9133) SS BOND : bond 0.00437 / 0.30 ( 10) SS BOND : angle 1.24922 / 0.85 ( 20) hydrogen bonds : bond 0.03864 / 2.52 ( 164) hydrogen bonds : angle 6.18345 / 4.09 ( 405) link_NAG-ASN : bond 0.00596 / 0.30 ( 3) link_NAG-ASN : angle 1.80293 / 0.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.6807 (p) cc_final: 0.6402 (p) REVERT: A 386 LYS cc_start: 0.8191 (tppt) cc_final: 0.7187 (tttt) REVERT: B 41 LYS cc_start: 0.8280 (mtpt) cc_final: 0.6392 (tptt) REVERT: B 134 GLN cc_start: 0.6314 (tp40) cc_final: 0.5765 (pm20) REVERT: B 237 ARG cc_start: 0.7855 (mtm180) cc_final: 0.6532 (ttm-80) REVERT: H 186 LEU cc_start: 0.8558 (mp) cc_final: 0.8254 (mt) REVERT: L 11 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7939 (tt) REVERT: L 109 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.5973 (ppp80) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 0.0987 time to fit residues: 15.7511 Evaluate side-chains 114 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 186 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.0010 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 199 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 = 0.3680 r_free = 0.3680 target = 0.146093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103052 restraints weight = 8311.518| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.51 r_work: 0.3003 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6733 Z= 0.160 Angle : 0.624 7.593 9162 Z= 0.319 Chirality : 0.047 0.317 1023 Planarity : 0.006 0.059 1164 Dihedral : 5.363 54.315 887 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.89 % Allowed : 8.54 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.64 (0.28), residues: 787 helix: -2.78 (0.74), residues: 26 sheet: -0.72 (0.33), residues: 261 loop : -2.40 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.021 0.002 TYR L 141 PHE 0.015 0.001 PHE B 238 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 6720) covalent geometry : angle 0.62184 / 0.32 ( 9133) SS BOND : bond 0.00318 / 0.22 ( 10) SS BOND : angle 0.90670 / 0.64 ( 20) hydrogen bonds : bond 0.03282 / 2.12 ( 164) hydrogen bonds : angle 5.80570 / 3.84 ( 405) link_NAG-ASN : bond 0.00442 / 0.23 ( 3) link_NAG-ASN : angle 1.45078 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7070 (pt) REVERT: A 361 CYS cc_start: 0.6767 (p) cc_final: 0.6237 (p) REVERT: A 386 LYS cc_start: 0.8223 (tppt) cc_final: 0.7246 (tttt) REVERT: A 586 ASP cc_start: 0.8113 (m-30) cc_final: 0.7765 (m-30) REVERT: B 41 LYS cc_start: 0.8251 (mtpt) cc_final: 0.6398 (tptt) REVERT: B 134 GLN cc_start: 0.6377 (tp40) cc_final: 0.5846 (pm20) REVERT: B 202 LYS cc_start: 0.8634 (mttp) cc_final: 0.7981 (mtpm) REVERT: B 237 ARG cc_start: 0.7842 (mtm180) cc_final: 0.6517 (ttm-80) REVERT: H 186 LEU cc_start: 0.8575 (mp) cc_final: 0.8269 (mt) REVERT: L 11 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7935 (tt) REVERT: L 168 ASP cc_start: 0.7487 (t0) cc_final: 0.7108 (t0) outliers start: 21 outliers final: 17 residues processed: 128 average time/residue: 0.0933 time to fit residues: 15.5696 Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 186 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 9 optimal weight: 0.0030 chunk 47 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN ** L 199 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 = 0.3708 r_free = 0.3708 target = 0.148464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105360 restraints weight = 8377.759| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.54 r_work: 0.3038 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6733 Z= 0.102 Angle : 0.559 7.277 9162 Z= 0.283 Chirality : 0.045 0.295 1023 Planarity : 0.005 0.061 1164 Dihedral : 4.901 52.461 887 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.48 % Allowed : 9.78 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.25 (0.29), residues: 787 helix: -2.55 (0.80), residues: 26 sheet: -0.47 (0.33), residues: 270 loop : -2.14 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.019 0.001 TYR L 141 PHE 0.012 0.001 PHE B 238 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 6720) covalent geometry : angle 0.55725 / 0.28 ( 9133) SS BOND : bond 0.00189 / 0.12 ( 10) SS BOND : angle 0.67735 / 0.47 ( 20) hydrogen bonds : bond 0.02697 / 1.74 ( 164) hydrogen bonds : angle 5.44538 / 3.60 ( 405) link_NAG-ASN : bond 0.00434 / 0.23 ( 3) link_NAG-ASN : angle 1.27520 / 0.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8197 (tppt) cc_final: 0.7290 (tttt) REVERT: A 586 ASP cc_start: 0.8059 (m-30) cc_final: 0.7692 (m-30) REVERT: B 41 LYS cc_start: 0.8139 (mtpt) cc_final: 0.6257 (tptt) REVERT: B 101 ILE cc_start: 0.8580 (mm) cc_final: 0.8346 (mm) REVERT: B 134 GLN cc_start: 0.6404 (tp40) cc_final: 0.5822 (pm20) REVERT: B 237 ARG cc_start: 0.7804 (mtm180) cc_final: 0.6468 (ttm-80) REVERT: H 159 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7712 (mt-10) REVERT: H 186 LEU cc_start: 0.8495 (mp) cc_final: 0.8206 (mt) REVERT: L 168 ASP cc_start: 0.7442 (t0) cc_final: 0.7040 (t0) outliers start: 18 outliers final: 14 residues processed: 127 average time/residue: 0.0876 time to fit residues: 14.6348 Evaluate side-chains 126 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104547 restraints weight = 8351.690| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.51 r_work: 0.3044 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6733 Z= 0.120 Angle : 0.564 7.100 9162 Z= 0.286 Chirality : 0.045 0.292 1023 Planarity : 0.005 0.059 1164 Dihedral : 4.849 51.755 887 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.75 % Allowed : 11.16 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.06 (0.29), residues: 787 helix: -2.44 (0.82), residues: 26 sheet: -0.28 (0.33), residues: 268 loop : -2.05 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.017 0.001 TYR L 141 PHE 0.012 0.001 PHE B 238 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 6720) covalent geometry : angle 0.56231 / 0.29 ( 9133) SS BOND : bond 0.00281 / 0.18 ( 10) SS BOND : angle 0.73772 / 0.50 ( 20) hydrogen bonds : bond 0.02784 / 1.79 ( 164) hydrogen bonds : angle 5.37196 / 3.55 ( 405) link_NAG-ASN : bond 0.00446 / 0.23 ( 3) link_NAG-ASN : angle 1.23837 / 0.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7111 (pt) REVERT: A 386 LYS cc_start: 0.8182 (tppt) cc_final: 0.7321 (tttt) REVERT: A 586 ASP cc_start: 0.8103 (m-30) cc_final: 0.7756 (m-30) REVERT: B 41 LYS cc_start: 0.8130 (mtpt) cc_final: 0.6242 (tptt) REVERT: B 101 ILE cc_start: 0.8593 (mm) cc_final: 0.8347 (mm) REVERT: B 134 GLN cc_start: 0.6442 (tp40) cc_final: 0.5884 (pm20) REVERT: B 202 LYS cc_start: 0.8671 (mttp) cc_final: 0.8009 (mtpm) REVERT: B 237 ARG cc_start: 0.7837 (mtm180) cc_final: 0.6574 (mtm-85) REVERT: H 159 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7751 (mt-10) REVERT: H 186 LEU cc_start: 0.8497 (mp) cc_final: 0.8216 (mt) REVERT: L 11 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7940 (tt) REVERT: L 17 GLU cc_start: 0.8355 (tp30) cc_final: 0.8130 (tp30) REVERT: L 168 ASP cc_start: 0.7488 (t0) cc_final: 0.7093 (t0) outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 0.0893 time to fit residues: 14.7935 Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102750 restraints weight = 8307.987| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.51 r_work: 0.3000 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6733 Z= 0.156 Angle : 0.591 7.318 9162 Z= 0.302 Chirality : 0.046 0.266 1023 Planarity : 0.005 0.060 1164 Dihedral : 4.976 51.499 887 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.75 % Allowed : 10.88 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.29), residues: 787 helix: -2.30 (0.83), residues: 26 sheet: -0.28 (0.33), residues: 274 loop : -1.99 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.019 0.002 TYR A 495 PHE 0.013 0.001 PHE B 238 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6720) covalent geometry : angle 0.58879 / 0.30 ( 9133) SS BOND : bond 0.00326 / 0.23 ( 10) SS BOND : angle 0.86861 / 0.58 ( 20) hydrogen bonds : bond 0.03010 / 1.95 ( 164) hydrogen bonds : angle 5.40299 / 3.59 ( 405) link_NAG-ASN : bond 0.00396 / 0.21 ( 3) link_NAG-ASN : angle 1.28133 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6992 (pt) REVERT: A 361 CYS cc_start: 0.6801 (p) cc_final: 0.6306 (p) REVERT: A 386 LYS cc_start: 0.8153 (tppt) cc_final: 0.7373 (tttt) REVERT: A 553 THR cc_start: 0.8338 (p) cc_final: 0.8076 (t) REVERT: A 586 ASP cc_start: 0.8050 (m-30) cc_final: 0.7710 (m-30) REVERT: B 41 LYS cc_start: 0.8156 (mtpt) cc_final: 0.6264 (tptt) REVERT: B 101 ILE cc_start: 0.8621 (mm) cc_final: 0.8377 (mm) REVERT: B 134 GLN cc_start: 0.6506 (tp40) cc_final: 0.5931 (pm20) REVERT: B 202 LYS cc_start: 0.8706 (mttp) cc_final: 0.8066 (mtpm) REVERT: H 159 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7814 (mt-10) REVERT: H 186 LEU cc_start: 0.8524 (mp) cc_final: 0.8268 (mt) REVERT: L 11 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7900 (tt) REVERT: L 17 GLU cc_start: 0.8346 (tp30) cc_final: 0.8075 (tp30) REVERT: L 168 ASP cc_start: 0.7499 (t0) cc_final: 0.7104 (t0) outliers start: 20 outliers final: 17 residues processed: 125 average time/residue: 0.0854 time to fit residues: 14.0752 Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106287 restraints weight = 8333.872| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.52 r_work: 0.3045 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6733 Z= 0.095 Angle : 0.536 7.079 9162 Z= 0.270 Chirality : 0.044 0.272 1023 Planarity : 0.005 0.057 1164 Dihedral : 4.626 50.180 887 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.89 % Allowed : 10.61 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.30), residues: 787 helix: -2.25 (0.85), residues: 26 sheet: -0.11 (0.33), residues: 275 loop : -1.88 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.013 0.001 TYR L 141 PHE 0.012 0.001 PHE B 238 TRP 0.013 0.001 TRP L 94 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6720) covalent geometry : angle 0.53510 / 0.27 ( 9133) SS BOND : bond 0.00214 / 0.13 ( 10) SS BOND : angle 0.58371 / 0.40 ( 20) hydrogen bonds : bond 0.02520 / 1.62 ( 164) hydrogen bonds : angle 5.15645 / 3.44 ( 405) link_NAG-ASN : bond 0.00414 / 0.22 ( 3) link_NAG-ASN : angle 1.10147 / 0.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7676 (pm20) cc_final: 0.7341 (pt0) REVERT: A 386 LYS cc_start: 0.8149 (tppt) cc_final: 0.7432 (tttt) REVERT: A 586 ASP cc_start: 0.7965 (m-30) cc_final: 0.7612 (m-30) REVERT: B 41 LYS cc_start: 0.8035 (mtpt) cc_final: 0.6160 (tptt) REVERT: B 101 ILE cc_start: 0.8604 (mm) cc_final: 0.8372 (mm) REVERT: B 134 GLN cc_start: 0.6493 (tp40) cc_final: 0.5934 (pm20) REVERT: B 202 LYS cc_start: 0.8660 (mttp) cc_final: 0.8006 (mtpm) REVERT: B 237 ARG cc_start: 0.7868 (mtm180) cc_final: 0.6563 (mtm-85) REVERT: H 159 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7847 (mt-10) REVERT: H 186 LEU cc_start: 0.8482 (mp) cc_final: 0.7785 (mt) REVERT: L 11 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7845 (tt) REVERT: L 17 GLU cc_start: 0.8266 (tp30) cc_final: 0.7895 (tp30) REVERT: L 168 ASP cc_start: 0.7483 (t0) cc_final: 0.7107 (t0) outliers start: 21 outliers final: 16 residues processed: 130 average time/residue: 0.0827 time to fit residues: 14.2632 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS ** L 199 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 = 0.3691 r_free = 0.3691 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104113 restraints weight = 8381.599| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.53 r_work: 0.3037 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6733 Z= 0.122 Angle : 0.556 7.261 9162 Z= 0.282 Chirality : 0.045 0.264 1023 Planarity : 0.005 0.095 1164 Dihedral : 4.703 49.758 887 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.62 % Allowed : 10.88 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.30), residues: 787 helix: -2.14 (0.85), residues: 26 sheet: 0.08 (0.33), residues: 267 loop : -1.82 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.015 0.001 TYR A 495 PHE 0.013 0.001 PHE B 238 TRP 0.010 0.001 TRP A 436 HIS 0.014 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6720) covalent geometry : angle 0.55427 / 0.28 ( 9133) SS BOND : bond 0.00276 / 0.18 ( 10) SS BOND : angle 0.72001 / 0.48 ( 20) hydrogen bonds : bond 0.02694 / 1.73 ( 164) hydrogen bonds : angle 5.16533 / 3.44 ( 405) link_NAG-ASN : bond 0.00383 / 0.20 ( 3) link_NAG-ASN : angle 1.17238 / 0.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8129 (tppt) cc_final: 0.7379 (tttt) REVERT: A 586 ASP cc_start: 0.7960 (m-30) cc_final: 0.7615 (m-30) REVERT: B 41 LYS cc_start: 0.8067 (mtpt) cc_final: 0.6180 (tptt) REVERT: B 101 ILE cc_start: 0.8622 (mm) cc_final: 0.8376 (mm) REVERT: B 134 GLN cc_start: 0.6549 (tp40) cc_final: 0.6015 (pm20) REVERT: B 202 LYS cc_start: 0.8695 (mttp) cc_final: 0.8024 (mtpm) REVERT: B 237 ARG cc_start: 0.7866 (mtm180) cc_final: 0.6556 (mtm-85) REVERT: H 159 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7835 (mt-10) REVERT: H 186 LEU cc_start: 0.8432 (mp) cc_final: 0.8105 (mt) REVERT: L 11 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7895 (tt) REVERT: L 17 GLU cc_start: 0.8258 (tp30) cc_final: 0.7956 (tp30) REVERT: L 168 ASP cc_start: 0.7489 (t0) cc_final: 0.7115 (t0) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.0838 time to fit residues: 13.6380 Evaluate side-chains 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.0040 chunk 35 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS ** L 199 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 = 0.3728 r_free = 0.3728 target = 0.150418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107619 restraints weight = 8170.258| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.48 r_work: 0.3066 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6733 Z= 0.086 Angle : 0.522 7.345 9162 Z= 0.263 Chirality : 0.044 0.265 1023 Planarity : 0.005 0.086 1164 Dihedral : 4.431 48.719 887 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.20 % Allowed : 11.16 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.30), residues: 787 helix: -2.14 (0.85), residues: 26 sheet: 0.18 (0.33), residues: 271 loop : -1.71 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.012 0.001 TYR L 141 PHE 0.011 0.001 PHE L 99 TRP 0.015 0.001 TRP L 94 HIS 0.013 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 ( 6720) covalent geometry : angle 0.52145 / 0.26 ( 9133) SS BOND : bond 0.00179 / 0.11 ( 10) SS BOND : angle 0.51561 / 0.35 ( 20) hydrogen bonds : bond 0.02384 / 1.52 ( 164) hydrogen bonds : angle 4.97237 / 3.32 ( 405) link_NAG-ASN : bond 0.00415 / 0.22 ( 3) link_NAG-ASN : angle 1.03699 / 0.55 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8059 (tppt) cc_final: 0.7331 (tttt) REVERT: A 586 ASP cc_start: 0.7907 (m-30) cc_final: 0.7580 (m-30) REVERT: B 41 LYS cc_start: 0.7931 (mtpt) cc_final: 0.6090 (tptt) REVERT: B 101 ILE cc_start: 0.8592 (mm) cc_final: 0.8360 (mm) REVERT: B 134 GLN cc_start: 0.6573 (tp40) cc_final: 0.6025 (pm20) REVERT: B 202 LYS cc_start: 0.8633 (mttp) cc_final: 0.7959 (mtpm) REVERT: B 237 ARG cc_start: 0.7827 (mtm180) cc_final: 0.6559 (mtm-85) REVERT: H 159 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7816 (mt-10) REVERT: H 186 LEU cc_start: 0.8370 (mp) cc_final: 0.8004 (mt) REVERT: L 11 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7821 (tt) REVERT: L 17 GLU cc_start: 0.8244 (tp30) cc_final: 0.7897 (tp30) REVERT: L 168 ASP cc_start: 0.7468 (t0) cc_final: 0.7091 (t0) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 0.0834 time to fit residues: 14.1470 Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 0.0060 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105594 restraints weight = 8311.785| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.50 r_work: 0.3040 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6733 Z= 0.108 Angle : 0.534 7.418 9162 Z= 0.271 Chirality : 0.044 0.260 1023 Planarity : 0.005 0.088 1164 Dihedral : 4.490 48.081 887 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.34 % Allowed : 11.16 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.30), residues: 787 helix: -2.02 (0.86), residues: 26 sheet: 0.08 (0.33), residues: 279 loop : -1.64 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.014 0.001 TYR A 495 PHE 0.022 0.001 PHE B 157 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6720) covalent geometry : angle 0.53359 / 0.27 ( 9133) SS BOND : bond 0.00234 / 0.16 ( 10) SS BOND : angle 0.64981 / 0.43 ( 20) hydrogen bonds : bond 0.02557 / 1.64 ( 164) hydrogen bonds : angle 5.02239 / 3.36 ( 405) link_NAG-ASN : bond 0.00383 / 0.20 ( 3) link_NAG-ASN : angle 0.97218 / 0.50 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.76 seconds wall clock time: 37 minutes 33.47 seconds (2253.47 seconds total)