Starting phenix.real_space_refine on Tue Mar 3 15:20:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u9o_26402/03_2026/7u9o_26402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u9o_26402/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7u9o_26402/03_2026/7u9o_26402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u9o_26402/03_2026/7u9o_26402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u9o_26402/03_2026/7u9o_26402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u9o_26402/03_2026/7u9o_26402.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.51, per 1000 atoms: 0.23 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 175.5 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: 0.25 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: 0.99 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: 3788 15.35 - 30.69: 167 30.69 - 46.04: 44 46.04 - 61.39: 6 61.39 - 76.73: 6 Dihedral angle restraints: 4011 sinusoidal: 1615 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 4008 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.530 Find NCS groups from input model: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 10.076 76.733 2437 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 covalent geometry : bond 0.00721 ( 6720) covalent geometry : angle 0.92126 ( 9133) SS BOND : bond 0.00714 ( 10) SS BOND : angle 2.08299 ( 20) hydrogen bonds : bond 0.27128 ( 164) hydrogen bonds : angle 10.35878 ( 405) link_NAG-ASN : bond 0.00439 ( 3) link_NAG-ASN : angle 3.67077 ( 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 : 0.221 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: 0.0950 time to fit residues: 20.9541 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 : 0.211 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 542 ASN A 556 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109049 restraints weight = 8195.003| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.69 r_work: 0.3078 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6733 Z= 0.106 Angle : 0.652 14.312 9162 Z= 0.327 Chirality : 0.046 0.175 1023 Planarity : 0.006 0.068 1164 Dihedral : 7.532 61.532 951 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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: -3.26 (0.28), residues: 787 helix: -4.04 (0.42), residues: 26 sheet: -1.14 (0.32), residues: 273 loop : -2.82 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.014 0.001 TYR L 174 PHE 0.013 0.001 PHE B 220 TRP 0.011 0.001 TRP H 50 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6720) covalent geometry : angle 0.64008 ( 9133) SS BOND : bond 0.00348 ( 10) SS BOND : angle 0.86998 ( 20) hydrogen bonds : bond 0.03714 ( 164) hydrogen bonds : angle 6.90552 ( 405) link_NAG-ASN : bond 0.00181 ( 3) link_NAG-ASN : angle 3.85041 ( 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 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.6535 (p) cc_final: 0.6105 (p) REVERT: A 525 CYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6674 (m) REVERT: B 41 LYS cc_start: 0.8138 (mtpt) cc_final: 0.6351 (tptt) REVERT: B 134 GLN cc_start: 0.6162 (tp40) cc_final: 0.5663 (pm20) REVERT: B 237 ARG cc_start: 0.7693 (mtm180) cc_final: 0.6392 (ttm-80) REVERT: B 278 LYS cc_start: 0.8212 (tttt) cc_final: 0.7995 (tttt) REVERT: H 116 GLN cc_start: 0.8586 (pm20) cc_final: 0.8090 (pm20) REVERT: H 149 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8037 (pp) REVERT: H 220 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7558 (tpp-160) REVERT: L 11 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7928 (tt) REVERT: L 177 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8580 (m) outliers start: 14 outliers final: 7 residues processed: 130 average time/residue: 0.0844 time to fit residues: 14.2522 Evaluate side-chains 121 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN 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 149 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 177 SER 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: 6.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3664 r_free = 0.3664 target = 0.144657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101619 restraints weight = 8289.833| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.49 r_work: 0.2976 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6733 Z= 0.238 Angle : 0.725 11.412 9162 Z= 0.370 Chirality : 0.050 0.248 1023 Planarity : 0.007 0.069 1164 Dihedral : 8.037 76.001 951 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.17 % Allowed : 7.44 % Favored : 89.39 % 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: -3.00 (0.28), residues: 787 helix: -3.25 (0.62), residues: 26 sheet: -1.12 (0.33), residues: 258 loop : -2.54 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 34 TYR 0.028 0.003 TYR A 495 PHE 0.022 0.002 PHE A 347 TRP 0.017 0.002 TRP H 114 HIS 0.009 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 6720) covalent geometry : angle 0.71628 ( 9133) SS BOND : bond 0.00496 ( 10) SS BOND : angle 1.29939 ( 20) hydrogen bonds : bond 0.04101 ( 164) hydrogen bonds : angle 6.21646 ( 405) link_NAG-ASN : bond 0.00351 ( 3) link_NAG-ASN : angle 3.32857 ( 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 137 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7180 (pt) REVERT: A 386 LYS cc_start: 0.8199 (tppt) cc_final: 0.7090 (tttt) REVERT: A 586 ASP cc_start: 0.8128 (m-30) cc_final: 0.7749 (m-30) REVERT: B 41 LYS cc_start: 0.8317 (mtpt) cc_final: 0.6435 (tptt) REVERT: B 134 GLN cc_start: 0.6328 (tp40) cc_final: 0.5812 (pm20) REVERT: B 237 ARG cc_start: 0.7879 (mtm180) cc_final: 0.6558 (ttm-80) REVERT: L 11 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7995 (tt) REVERT: L 17 GLU cc_start: 0.8454 (tp30) cc_final: 0.8233 (tp30) REVERT: L 109 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6024 (ppp80) outliers start: 23 outliers final: 15 residues processed: 131 average time/residue: 0.0837 time to fit residues: 14.2636 Evaluate side-chains 122 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN 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 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 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 106 THR Chi-restraints excluded: chain H residue 164 SER 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 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: 0.3980 chunk 58 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3708 r_free = 0.3708 target = 0.148549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105281 restraints weight = 8279.163| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.53 r_work: 0.3030 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6733 Z= 0.104 Angle : 0.596 11.320 9162 Z= 0.298 Chirality : 0.045 0.254 1023 Planarity : 0.005 0.060 1164 Dihedral : 7.611 79.188 950 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.93 % Allowed : 10.33 % 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: -2.49 (0.29), residues: 787 helix: -2.88 (0.73), residues: 26 sheet: -0.60 (0.33), residues: 269 loop : -2.32 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.021 0.001 TYR L 141 PHE 0.013 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 covalent geometry : bond 0.00232 ( 6720) covalent geometry : angle 0.58957 ( 9133) SS BOND : bond 0.00227 ( 10) SS BOND : angle 0.71467 ( 20) hydrogen bonds : bond 0.02889 ( 164) hydrogen bonds : angle 5.65825 ( 405) link_NAG-ASN : bond 0.00480 ( 3) link_NAG-ASN : angle 2.83168 ( 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 131 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8135 (tppt) cc_final: 0.7126 (tttt) REVERT: A 586 ASP cc_start: 0.7988 (m-30) cc_final: 0.7669 (m-30) REVERT: B 41 LYS cc_start: 0.8145 (mtpt) cc_final: 0.6288 (tptt) REVERT: B 134 GLN cc_start: 0.6396 (tp40) cc_final: 0.5847 (pm20) REVERT: B 237 ARG cc_start: 0.7614 (mtm180) cc_final: 0.6305 (ttm-80) REVERT: H 186 LEU cc_start: 0.8538 (mp) cc_final: 0.8242 (mt) REVERT: L 17 GLU cc_start: 0.8190 (tp30) cc_final: 0.7952 (tp30) outliers start: 14 outliers final: 12 residues processed: 125 average time/residue: 0.0833 time to fit residues: 13.7167 Evaluate side-chains 120 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR 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 106 THR Chi-restraints excluded: chain H residue 222 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 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: 0.0050 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 overall best weight: 0.1910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN H 2 GLN ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108015 restraints weight = 8360.867| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.54 r_work: 0.3182 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6733 Z= 0.082 Angle : 0.544 10.702 9162 Z= 0.269 Chirality : 0.044 0.249 1023 Planarity : 0.005 0.064 1164 Dihedral : 7.102 82.149 950 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.20 % Allowed : 10.47 % Favored : 87.33 % 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: -2.04 (0.29), residues: 787 helix: -2.50 (0.89), residues: 20 sheet: -0.29 (0.32), residues: 274 loop : -2.04 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.017 0.001 TYR L 141 PHE 0.021 0.001 PHE B 157 TRP 0.010 0.001 TRP L 94 HIS 0.002 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 6720) covalent geometry : angle 0.53795 ( 9133) SS BOND : bond 0.00183 ( 10) SS BOND : angle 0.64522 ( 20) hydrogen bonds : bond 0.02462 ( 164) hydrogen bonds : angle 5.24042 ( 405) link_NAG-ASN : bond 0.00451 ( 3) link_NAG-ASN : angle 2.56684 ( 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 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8154 (tppt) cc_final: 0.7195 (tttt) REVERT: A 506 GLN cc_start: 0.9120 (mt0) cc_final: 0.8642 (mt0) REVERT: A 580 GLN cc_start: 0.8870 (mt0) cc_final: 0.8640 (mm-40) REVERT: A 586 ASP cc_start: 0.8074 (m-30) cc_final: 0.7762 (m-30) REVERT: B 41 LYS cc_start: 0.8028 (mtpt) cc_final: 0.6235 (tptt) REVERT: B 101 ILE cc_start: 0.8576 (mm) cc_final: 0.8341 (mm) REVERT: B 134 GLN cc_start: 0.6338 (tp40) cc_final: 0.5799 (pm20) REVERT: B 237 ARG cc_start: 0.7747 (mtm180) cc_final: 0.6513 (ttm-80) REVERT: H 159 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7641 (mt-10) REVERT: H 186 LEU cc_start: 0.8527 (mp) cc_final: 0.8092 (mt) REVERT: L 11 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7950 (tt) REVERT: L 17 GLU cc_start: 0.8171 (tp30) cc_final: 0.7938 (tp30) REVERT: L 168 ASP cc_start: 0.7417 (t70) cc_final: 0.7049 (t0) outliers start: 16 outliers final: 11 residues processed: 130 average time/residue: 0.0786 time to fit residues: 13.5301 Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR 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 106 THR Chi-restraints excluded: chain H residue 164 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3668 r_free = 0.3668 target = 0.145310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104508 restraints weight = 8393.404| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.56 r_work: 0.2999 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6733 Z= 0.179 Angle : 0.631 10.677 9162 Z= 0.318 Chirality : 0.047 0.205 1023 Planarity : 0.005 0.060 1164 Dihedral : 7.000 75.747 950 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.44 % Allowed : 10.61 % Favored : 85.95 % 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: -2.41 (0.83), residues: 26 sheet: -0.28 (0.32), residues: 274 loop : -1.99 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.021 0.002 TYR A 495 PHE 0.018 0.002 PHE A 541 TRP 0.010 0.002 TRP H 114 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6720) covalent geometry : angle 0.62421 ( 9133) SS BOND : bond 0.00365 ( 10) SS BOND : angle 1.13714 ( 20) hydrogen bonds : bond 0.03140 ( 164) hydrogen bonds : angle 5.44266 ( 405) link_NAG-ASN : bond 0.00316 ( 3) link_NAG-ASN : angle 2.55288 ( 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 137 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8199 (tppt) cc_final: 0.7248 (tttt) REVERT: A 586 ASP cc_start: 0.8047 (m-30) cc_final: 0.7674 (m-30) REVERT: B 41 LYS cc_start: 0.8157 (mtpt) cc_final: 0.6244 (tptt) REVERT: B 101 ILE cc_start: 0.8603 (mm) cc_final: 0.8357 (mm) REVERT: B 134 GLN cc_start: 0.6471 (tp40) cc_final: 0.5896 (pm20) REVERT: B 202 LYS cc_start: 0.8707 (mttp) cc_final: 0.8032 (mtpm) REVERT: H 149 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7895 (pt) REVERT: H 159 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7786 (mt-10) REVERT: H 186 LEU cc_start: 0.8518 (mp) cc_final: 0.8258 (mt) REVERT: L 11 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7899 (tt) REVERT: L 17 GLU cc_start: 0.8206 (tp30) cc_final: 0.7882 (tp30) REVERT: L 168 ASP cc_start: 0.7445 (t70) cc_final: 0.7097 (t0) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.0803 time to fit residues: 13.8384 Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL 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 149 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 66 optimal weight: 0.0030 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3699 r_free = 0.3699 target = 0.147857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105004 restraints weight = 8299.253| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.51 r_work: 0.3031 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6733 Z= 0.110 Angle : 0.575 10.713 9162 Z= 0.284 Chirality : 0.045 0.198 1023 Planarity : 0.005 0.060 1164 Dihedral : 6.511 71.121 950 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.89 % Allowed : 11.02 % 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: -1.81 (0.29), residues: 787 helix: -2.38 (0.84), 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 0.002 0.000 ARG B 34 TYR 0.015 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 covalent geometry : bond 0.00259 ( 6720) covalent geometry : angle 0.56951 ( 9133) SS BOND : bond 0.00324 ( 10) SS BOND : angle 0.76066 ( 20) hydrogen bonds : bond 0.02662 ( 164) hydrogen bonds : angle 5.28718 ( 405) link_NAG-ASN : bond 0.00294 ( 3) link_NAG-ASN : angle 2.57636 ( 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 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 VAL cc_start: 0.9017 (t) cc_final: 0.8755 (m) REVERT: A 386 LYS cc_start: 0.8228 (tppt) cc_final: 0.7299 (tttt) REVERT: A 586 ASP cc_start: 0.8046 (m-30) cc_final: 0.7690 (m-30) REVERT: B 41 LYS cc_start: 0.8057 (mtpt) cc_final: 0.6178 (tptt) REVERT: B 101 ILE cc_start: 0.8545 (mm) cc_final: 0.8304 (mm) REVERT: B 134 GLN cc_start: 0.6477 (tp40) cc_final: 0.5923 (pm20) REVERT: B 202 LYS cc_start: 0.8667 (mttp) cc_final: 0.8010 (mtpm) REVERT: B 237 ARG cc_start: 0.7807 (mtm180) cc_final: 0.6589 (mtm-85) REVERT: H 159 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7933 (mt-10) REVERT: H 186 LEU cc_start: 0.8467 (mp) cc_final: 0.8236 (mt) REVERT: L 11 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7894 (tt) REVERT: L 168 ASP cc_start: 0.7434 (t70) cc_final: 0.7081 (t0) outliers start: 21 outliers final: 18 residues processed: 125 average time/residue: 0.0832 time to fit residues: 13.6916 Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN 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 549 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 287 ASP 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 0.0270 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3714 r_free = 0.3714 target = 0.149244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106105 restraints weight = 8367.216| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.54 r_work: 0.3048 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3257 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= 0.093 Angle : 0.552 10.334 9162 Z= 0.271 Chirality : 0.043 0.155 1023 Planarity : 0.005 0.058 1164 Dihedral : 5.794 59.306 950 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.62 % Allowed : 11.57 % Favored : 85.81 % 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: -1.61 (0.30), residues: 787 helix: -2.12 (0.94), residues: 20 sheet: 0.07 (0.33), residues: 275 loop : -1.81 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 34 TYR 0.013 0.001 TYR L 141 PHE 0.011 0.001 PHE B 238 TRP 0.011 0.001 TRP L 94 HIS 0.014 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6720) covalent geometry : angle 0.54412 ( 9133) SS BOND : bond 0.00165 ( 10) SS BOND : angle 0.69728 ( 20) hydrogen bonds : bond 0.02487 ( 164) hydrogen bonds : angle 5.06906 ( 405) link_NAG-ASN : bond 0.00236 ( 3) link_NAG-ASN : angle 2.91177 ( 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 132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 VAL cc_start: 0.9014 (t) cc_final: 0.8780 (m) REVERT: A 386 LYS cc_start: 0.8177 (tppt) cc_final: 0.7382 (tttt) REVERT: A 586 ASP cc_start: 0.7887 (m-30) cc_final: 0.7571 (m-30) REVERT: B 41 LYS cc_start: 0.7924 (mtpt) cc_final: 0.6088 (tptt) REVERT: B 101 ILE cc_start: 0.8521 (mm) cc_final: 0.8292 (mm) REVERT: B 134 GLN cc_start: 0.6495 (tp40) cc_final: 0.5970 (pm20) REVERT: B 237 ARG cc_start: 0.7576 (mtm180) cc_final: 0.6401 (mtm-85) REVERT: H 159 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7763 (mt-10) REVERT: H 186 LEU cc_start: 0.8471 (mp) cc_final: 0.8235 (mt) REVERT: L 11 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7802 (tt) REVERT: L 168 ASP cc_start: 0.7407 (t70) cc_final: 0.7076 (t0) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 0.0826 time to fit residues: 13.4453 Evaluate side-chains 125 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER 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 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 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.0040 chunk 6 optimal weight: 2.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS L 6 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101772 restraints weight = 8357.972| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.50 r_work: 0.2988 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6733 Z= 0.194 Angle : 0.638 9.825 9162 Z= 0.321 Chirality : 0.047 0.183 1023 Planarity : 0.006 0.099 1164 Dihedral : 5.867 49.962 950 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.75 % Allowed : 11.57 % Favored : 85.67 % 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: -1.68 (0.30), residues: 787 helix: -2.18 (0.87), residues: 26 sheet: 0.03 (0.32), residues: 272 loop : -1.83 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.022 0.002 TYR A 495 PHE 0.014 0.002 PHE B 238 TRP 0.011 0.002 TRP H 50 HIS 0.013 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 6720) covalent geometry : angle 0.62865 ( 9133) SS BOND : bond 0.00380 ( 10) SS BOND : angle 1.14120 ( 20) hydrogen bonds : bond 0.03146 ( 164) hydrogen bonds : angle 5.38772 ( 405) link_NAG-ASN : bond 0.00204 ( 3) link_NAG-ASN : angle 3.27640 ( 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 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8246 (tppt) cc_final: 0.7375 (tttt) REVERT: A 586 ASP cc_start: 0.7992 (m-30) cc_final: 0.7653 (m-30) REVERT: B 41 LYS cc_start: 0.8125 (mtpt) cc_final: 0.6203 (tptt) REVERT: B 101 ILE cc_start: 0.8588 (mm) cc_final: 0.8343 (mm) REVERT: B 134 GLN cc_start: 0.6610 (tp40) cc_final: 0.5993 (pm20) REVERT: B 202 LYS cc_start: 0.8733 (mttp) cc_final: 0.8167 (mtpm) REVERT: B 237 ARG cc_start: 0.7873 (mtm180) cc_final: 0.6636 (mtm-85) REVERT: H 159 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7936 (mt-10) REVERT: H 186 LEU cc_start: 0.8504 (mp) cc_final: 0.8262 (mt) REVERT: L 11 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7955 (tt) REVERT: L 168 ASP cc_start: 0.7507 (t70) cc_final: 0.7177 (t0) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 0.0760 time to fit residues: 12.5547 Evaluate side-chains 124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN 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 B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 11 VAL 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 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: 0.9980 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3715 r_free = 0.3715 target = 0.149147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106459 restraints weight = 8190.484| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.47 r_work: 0.3039 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6733 Z= 0.101 Angle : 0.565 9.214 9162 Z= 0.279 Chirality : 0.044 0.170 1023 Planarity : 0.005 0.089 1164 Dihedral : 5.228 49.335 950 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.20 % Allowed : 12.12 % Favored : 85.67 % 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: -1.59 (0.30), residues: 787 helix: -2.74 (0.72), residues: 32 sheet: 0.14 (0.33), residues: 273 loop : -1.74 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.013 0.001 TYR L 141 PHE 0.011 0.001 PHE B 238 TRP 0.012 0.001 TRP L 94 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 6720) covalent geometry : angle 0.55478 ( 9133) SS BOND : bond 0.00187 ( 10) SS BOND : angle 0.70777 ( 20) hydrogen bonds : bond 0.02547 ( 164) hydrogen bonds : angle 5.14918 ( 405) link_NAG-ASN : bond 0.00162 ( 3) link_NAG-ASN : angle 3.36094 ( 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 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8183 (tppt) cc_final: 0.7315 (tttt) REVERT: A 506 GLN cc_start: 0.9139 (mt0) cc_final: 0.8630 (mt0) REVERT: A 586 ASP cc_start: 0.7912 (m-30) cc_final: 0.7597 (m-30) REVERT: B 41 LYS cc_start: 0.7999 (mtpt) cc_final: 0.6126 (tptt) REVERT: B 101 ILE cc_start: 0.8552 (mm) cc_final: 0.8317 (mm) REVERT: B 134 GLN cc_start: 0.6619 (tp40) cc_final: 0.6001 (pm20) REVERT: B 202 LYS cc_start: 0.8688 (mttp) cc_final: 0.8048 (mtpm) REVERT: B 237 ARG cc_start: 0.7760 (mtm180) cc_final: 0.6531 (mtm-85) REVERT: H 159 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7935 (mt-10) REVERT: H 186 LEU cc_start: 0.8446 (mp) cc_final: 0.8206 (mt) REVERT: L 11 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7898 (tt) REVERT: L 168 ASP cc_start: 0.7482 (t70) cc_final: 0.7151 (t0) outliers start: 16 outliers final: 14 residues processed: 123 average time/residue: 0.0773 time to fit residues: 12.4505 Evaluate side-chains 126 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN 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 B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 227 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.0050 chunk 3 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.2770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3747 r_free = 0.3747 target = 0.152118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109787 restraints weight = 8286.441| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.48 r_work: 0.3082 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3526 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 : 0.530 7.448 9162 Z= 0.262 Chirality : 0.043 0.166 1023 Planarity : 0.005 0.081 1164 Dihedral : 4.754 47.329 950 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.93 % Allowed : 12.40 % Favored : 85.67 % 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: -1.37 (0.30), residues: 787 helix: -2.44 (0.79), residues: 26 sheet: 0.28 (0.33), residues: 272 loop : -1.61 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.012 0.001 TYR H 32 PHE 0.010 0.001 PHE B 238 TRP 0.017 0.001 TRP L 94 HIS 0.002 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 6720) covalent geometry : angle 0.52188 ( 9133) SS BOND : bond 0.00158 ( 10) SS BOND : angle 0.56716 ( 20) hydrogen bonds : bond 0.02352 ( 164) hydrogen bonds : angle 4.87437 ( 405) link_NAG-ASN : bond 0.00217 ( 3) link_NAG-ASN : angle 3.02002 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.98 seconds wall clock time: 34 minutes 17.80 seconds (2057.80 seconds total)