Starting phenix.real_space_refine on Thu Jul 24 19:02:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u9o_26402/07_2025/7u9o_26402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u9o_26402/07_2025/7u9o_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_2025/7u9o_26402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2025/7u9o_26402.map" model { file = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2025/7u9o_26402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u9o_26402/07_2025/7u9o_26402.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.68, per 1000 atoms: 0.71 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: 1.38 Conformation dependent library (CDL) restraints added in 878.8 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: 0.88 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: 1.84 Time building geometry restraints manager: 1.72 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: 0.810 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.003 TRP H 114 HIS 0.020 0.004 HIS H 35 PHE 0.050 0.003 PHE A 347 TYR 0.037 0.004 TYR A 495 ARG 0.010 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 3) link_NAG-ASN : angle 3.67077 ( 9) hydrogen bonds : bond 0.27128 ( 164) hydrogen bonds : angle 10.35878 ( 405) SS BOND : bond 0.00714 ( 10) SS BOND : angle 2.08299 ( 20) covalent geometry : bond 0.00721 ( 6720) covalent geometry : angle 0.92126 ( 9133) *********************** 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 : 0.992 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.5699 (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: 0.7828 (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: 0.2629 time to fit residues: 58.5153 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 : 1.081 ------------------------------------------------------------------------------- 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 67 optimal weight: 0.0030 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106019 restraints weight = 8088.590| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.49 r_work: 0.3055 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6733 Z= 0.117 Angle : 0.651 13.877 9162 Z= 0.328 Chirality : 0.047 0.226 1023 Planarity : 0.006 0.069 1164 Dihedral : 7.681 65.029 951 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.20 % Allowed : 5.51 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.27), residues: 787 helix: -4.01 (0.43), residues: 26 sheet: -1.19 (0.33), residues: 262 loop : -2.78 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE B 220 TYR 0.015 0.002 TYR A 495 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 3) link_NAG-ASN : angle 2.36872 ( 9) hydrogen bonds : bond 0.03509 ( 164) hydrogen bonds : angle 6.85813 ( 405) SS BOND : bond 0.00295 ( 10) SS BOND : angle 0.89419 ( 20) covalent geometry : bond 0.00264 ( 6720) covalent geometry : angle 0.64617 ( 9133) *********************** 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: 16 poor density : 123 time to evaluate : 1.840 Fit side-chains REVERT: A 361 CYS cc_start: 0.6619 (p) cc_final: 0.6177 (p) REVERT: A 525 CYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6675 (m) REVERT: B 41 LYS cc_start: 0.8245 (mtpt) cc_final: 0.6394 (tptt) REVERT: B 134 GLN cc_start: 0.6125 (tp40) cc_final: 0.5648 (pm20) REVERT: B 237 ARG cc_start: 0.7757 (mtm180) cc_final: 0.6471 (ttm-80) REVERT: B 278 LYS cc_start: 0.8297 (tttt) cc_final: 0.8090 (tttt) REVERT: H 149 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8062 (pp) REVERT: H 220 ARG cc_start: 0.7898 (tpt170) cc_final: 0.7578 (tpp-160) REVERT: L 11 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7960 (tt) REVERT: L 177 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8611 (m) outliers start: 16 outliers final: 8 residues processed: 133 average time/residue: 0.3532 time to fit residues: 61.0308 Evaluate side-chains 121 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.145335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106748 restraints weight = 8243.382| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.39 r_work: 0.3007 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6733 Z= 0.218 Angle : 0.711 10.629 9162 Z= 0.363 Chirality : 0.049 0.193 1023 Planarity : 0.007 0.095 1164 Dihedral : 7.821 71.030 951 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.89 % Allowed : 7.30 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.28), residues: 787 helix: -3.20 (0.62), residues: 26 sheet: -1.10 (0.33), residues: 258 loop : -2.51 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 114 HIS 0.008 0.002 HIS H 35 PHE 0.019 0.002 PHE A 347 TYR 0.026 0.002 TYR A 495 ARG 0.005 0.001 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 3) link_NAG-ASN : angle 3.23206 ( 9) hydrogen bonds : bond 0.03961 ( 164) hydrogen bonds : angle 6.18003 ( 405) SS BOND : bond 0.00464 ( 10) SS BOND : angle 1.27724 ( 20) covalent geometry : bond 0.00533 ( 6720) covalent geometry : angle 0.70192 ( 9133) *********************** 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 131 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7108 (pt) REVERT: A 586 ASP cc_start: 0.8158 (m-30) cc_final: 0.7801 (m-30) REVERT: B 41 LYS cc_start: 0.8300 (mtpt) cc_final: 0.6437 (tptt) REVERT: B 134 GLN cc_start: 0.6309 (tp40) cc_final: 0.5837 (pm20) REVERT: H 186 LEU cc_start: 0.8549 (mp) cc_final: 0.8254 (mt) REVERT: L 11 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7986 (tt) REVERT: L 109 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5994 (ppp80) outliers start: 21 outliers final: 13 residues processed: 126 average time/residue: 0.1992 time to fit residues: 32.7622 Evaluate side-chains 117 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 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 73 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.144979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103229 restraints weight = 8337.428| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.59 r_work: 0.3026 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6733 Z= 0.204 Angle : 0.681 11.503 9162 Z= 0.345 Chirality : 0.048 0.214 1023 Planarity : 0.006 0.092 1164 Dihedral : 7.718 73.015 950 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.58 % Allowed : 8.95 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.28), residues: 787 helix: -2.76 (0.74), residues: 26 sheet: -0.92 (0.32), residues: 267 loop : -2.39 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.008 0.002 HIS H 35 PHE 0.016 0.002 PHE B 238 TYR 0.023 0.002 TYR A 495 ARG 0.005 0.001 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 3) link_NAG-ASN : angle 3.09664 ( 9) hydrogen bonds : bond 0.03545 ( 164) hydrogen bonds : angle 5.88863 ( 405) SS BOND : bond 0.00363 ( 10) SS BOND : angle 1.14657 ( 20) covalent geometry : bond 0.00496 ( 6720) covalent geometry : angle 0.67250 ( 9133) *********************** 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 140 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8225 (tppt) cc_final: 0.7082 (tttt) REVERT: A 586 ASP cc_start: 0.8180 (m-30) cc_final: 0.7840 (m-30) REVERT: B 41 LYS cc_start: 0.8305 (mtpt) cc_final: 0.6405 (tptt) REVERT: B 134 GLN cc_start: 0.6492 (tp40) cc_final: 0.5936 (pm20) REVERT: B 202 LYS cc_start: 0.8688 (mttp) cc_final: 0.8081 (mtpm) REVERT: H 159 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7777 (mt-10) REVERT: H 186 LEU cc_start: 0.8581 (mp) cc_final: 0.8286 (mt) REVERT: L 11 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8107 (tt) outliers start: 26 outliers final: 20 residues processed: 133 average time/residue: 0.2016 time to fit residues: 34.9393 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 503 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER 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 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 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 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3688 r_free = 0.3688 target = 0.146899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103881 restraints weight = 8290.111| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.50 r_work: 0.3017 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6733 Z= 0.118 Angle : 0.601 11.111 9162 Z= 0.301 Chirality : 0.045 0.213 1023 Planarity : 0.005 0.084 1164 Dihedral : 7.261 73.355 950 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.89 % Allowed : 10.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.29), residues: 787 helix: -2.55 (0.80), residues: 26 sheet: -0.51 (0.32), residues: 268 loop : -2.20 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.001 PHE B 238 TYR 0.020 0.001 TYR L 141 ARG 0.002 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 2.83373 ( 9) hydrogen bonds : bond 0.02922 ( 164) hydrogen bonds : angle 5.54651 ( 405) SS BOND : bond 0.00217 ( 10) SS BOND : angle 0.85525 ( 20) covalent geometry : bond 0.00278 ( 6720) covalent geometry : angle 0.59448 ( 9133) *********************** 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 136 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8136 (tppt) cc_final: 0.7080 (tttt) REVERT: A 586 ASP cc_start: 0.8075 (m-30) cc_final: 0.7696 (m-30) REVERT: B 105 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8544 (pt) REVERT: B 134 GLN cc_start: 0.6472 (tp40) cc_final: 0.5837 (pm20) REVERT: B 202 LYS cc_start: 0.8641 (mttp) cc_final: 0.7974 (mtpm) REVERT: H 159 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7763 (mt-10) REVERT: H 186 LEU cc_start: 0.8489 (mp) cc_final: 0.8193 (mt) REVERT: L 168 ASP cc_start: 0.7298 (t70) cc_final: 0.7044 (t0) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.2080 time to fit residues: 34.6615 Evaluate side-chains 124 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 ILE 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 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 222 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 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 0.0010 chunk 5 optimal weight: 0.0040 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.148714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108087 restraints weight = 8194.548| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.59 r_work: 0.3062 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6733 Z= 0.096 Angle : 0.565 10.923 9162 Z= 0.280 Chirality : 0.044 0.198 1023 Planarity : 0.005 0.089 1164 Dihedral : 6.618 68.903 950 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.62 % Allowed : 11.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.29), residues: 787 helix: -2.30 (0.86), residues: 26 sheet: -0.24 (0.33), residues: 269 loop : -1.98 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 94 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE B 238 TYR 0.017 0.001 TYR L 141 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 3) link_NAG-ASN : angle 2.82890 ( 9) hydrogen bonds : bond 0.02642 ( 164) hydrogen bonds : angle 5.19511 ( 405) SS BOND : bond 0.00234 ( 10) SS BOND : angle 0.72690 ( 20) covalent geometry : bond 0.00216 ( 6720) covalent geometry : angle 0.55794 ( 9133) *********************** 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 140 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8234 (tppt) cc_final: 0.7227 (tttt) REVERT: A 586 ASP cc_start: 0.8106 (m-30) cc_final: 0.7768 (m-30) REVERT: B 101 ILE cc_start: 0.8594 (mm) cc_final: 0.8347 (mm) REVERT: B 134 GLN cc_start: 0.6490 (tp40) cc_final: 0.5911 (pm20) REVERT: B 202 LYS cc_start: 0.8643 (mttp) cc_final: 0.8024 (mtpm) REVERT: H 159 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7816 (mt-10) REVERT: H 186 LEU cc_start: 0.8484 (mp) cc_final: 0.8238 (mt) REVERT: L 11 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7951 (tt) REVERT: L 17 GLU cc_start: 0.8317 (tp30) cc_final: 0.8022 (tp30) REVERT: L 168 ASP cc_start: 0.7277 (t70) cc_final: 0.7037 (t0) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 0.1915 time to fit residues: 33.7434 Evaluate side-chains 125 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 515 PHE 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 B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL 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 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 77 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.149201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106324 restraints weight = 8242.596| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.51 r_work: 0.3056 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6733 Z= 0.093 Angle : 0.556 10.538 9162 Z= 0.276 Chirality : 0.044 0.176 1023 Planarity : 0.005 0.085 1164 Dihedral : 6.151 61.943 950 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.89 % Allowed : 11.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.30), residues: 787 helix: -2.21 (0.86), residues: 26 sheet: -0.08 (0.33), residues: 273 loop : -1.85 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.015 0.002 HIS B 207 PHE 0.012 0.001 PHE B 238 TYR 0.015 0.001 TYR L 141 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 3) link_NAG-ASN : angle 2.90739 ( 9) hydrogen bonds : bond 0.02570 ( 164) hydrogen bonds : angle 5.10259 ( 405) SS BOND : bond 0.00171 ( 10) SS BOND : angle 0.68816 ( 20) covalent geometry : bond 0.00207 ( 6720) covalent geometry : angle 0.54837 ( 9133) *********************** 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 : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8211 (tppt) cc_final: 0.7224 (tttt) REVERT: A 586 ASP cc_start: 0.8059 (m-30) cc_final: 0.7706 (m-30) REVERT: B 41 LYS cc_start: 0.8058 (mtpt) cc_final: 0.6187 (tptt) REVERT: B 88 ASP cc_start: 0.8900 (m-30) cc_final: 0.8636 (m-30) REVERT: B 101 ILE cc_start: 0.8611 (mm) cc_final: 0.8366 (mm) REVERT: B 134 GLN cc_start: 0.6487 (tp40) cc_final: 0.5922 (pm20) REVERT: B 237 ARG cc_start: 0.7841 (mtm180) cc_final: 0.6607 (mtm-85) REVERT: H 159 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7858 (mt-10) REVERT: H 186 LEU cc_start: 0.8483 (mp) cc_final: 0.7831 (mt) REVERT: L 11 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7896 (tt) REVERT: L 17 GLU cc_start: 0.8268 (tp30) cc_final: 0.7905 (tp30) REVERT: L 18 ARG cc_start: 0.8256 (ttp-170) cc_final: 0.7973 (ttt90) REVERT: L 168 ASP cc_start: 0.7283 (t70) cc_final: 0.7041 (t0) outliers start: 21 outliers final: 15 residues processed: 126 average time/residue: 0.1986 time to fit residues: 33.0575 Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 B residue 51 THR Chi-restraints excluded: chain B residue 94 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 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 29 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.148234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105083 restraints weight = 8363.716| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.53 r_work: 0.3032 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6733 Z= 0.117 Angle : 0.571 10.169 9162 Z= 0.283 Chirality : 0.044 0.167 1023 Planarity : 0.005 0.085 1164 Dihedral : 5.894 54.428 950 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.31 % Allowed : 11.29 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.30), residues: 787 helix: -2.15 (0.86), residues: 26 sheet: 0.01 (0.33), residues: 267 loop : -1.82 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.014 0.002 HIS B 207 PHE 0.013 0.001 PHE B 238 TYR 0.014 0.001 TYR A 495 ARG 0.002 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 3) link_NAG-ASN : angle 3.07628 ( 9) hydrogen bonds : bond 0.02676 ( 164) hydrogen bonds : angle 5.10714 ( 405) SS BOND : bond 0.00230 ( 10) SS BOND : angle 0.81227 ( 20) covalent geometry : bond 0.00274 ( 6720) covalent geometry : angle 0.56191 ( 9133) *********************** 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 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8185 (tppt) cc_final: 0.7242 (tttt) REVERT: A 586 ASP cc_start: 0.7936 (m-30) cc_final: 0.7585 (m-30) REVERT: B 41 LYS cc_start: 0.8058 (mtpt) cc_final: 0.6161 (tptt) REVERT: B 101 ILE cc_start: 0.8604 (mm) cc_final: 0.8351 (mm) REVERT: B 134 GLN cc_start: 0.6539 (tp40) cc_final: 0.5916 (pm20) REVERT: B 202 LYS cc_start: 0.8687 (mttp) cc_final: 0.8053 (mtpm) REVERT: B 237 ARG cc_start: 0.7827 (mtm180) cc_final: 0.6567 (mtm-85) REVERT: H 159 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7842 (mt-10) REVERT: H 181 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8017 (tt) REVERT: H 186 LEU cc_start: 0.8381 (mp) cc_final: 0.8065 (mt) REVERT: L 11 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7862 (tt) REVERT: L 17 GLU cc_start: 0.8249 (tp30) cc_final: 0.7849 (tp30) REVERT: L 18 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7916 (ttt90) REVERT: L 168 ASP cc_start: 0.7193 (t70) cc_final: 0.6943 (t0) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.2082 time to fit residues: 34.4016 Evaluate side-chains 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 94 SER 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 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 181 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 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 47 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.145620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102778 restraints weight = 8336.490| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.47 r_work: 0.3004 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6733 Z= 0.150 Angle : 0.603 9.336 9162 Z= 0.302 Chirality : 0.045 0.173 1023 Planarity : 0.006 0.090 1164 Dihedral : 5.689 50.153 950 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.03 % Allowed : 11.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.30), residues: 787 helix: -2.04 (0.88), residues: 26 sheet: -0.10 (0.32), residues: 274 loop : -1.75 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.014 0.002 HIS B 207 PHE 0.014 0.001 PHE B 238 TYR 0.018 0.002 TYR A 495 ARG 0.003 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 3) link_NAG-ASN : angle 3.36261 ( 9) hydrogen bonds : bond 0.02942 ( 164) hydrogen bonds : angle 5.26537 ( 405) SS BOND : bond 0.00306 ( 10) SS BOND : angle 0.98688 ( 20) covalent geometry : bond 0.00361 ( 6720) covalent geometry : angle 0.59263 ( 9133) *********************** 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 132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7683 (pm20) cc_final: 0.7405 (pt0) REVERT: A 386 LYS cc_start: 0.8143 (tppt) cc_final: 0.7293 (tttt) REVERT: A 553 THR cc_start: 0.8331 (p) cc_final: 0.8089 (t) REVERT: A 586 ASP cc_start: 0.7970 (m-30) cc_final: 0.7654 (m-30) REVERT: B 101 ILE cc_start: 0.8631 (mm) cc_final: 0.8385 (mm) REVERT: B 134 GLN cc_start: 0.6595 (tp40) cc_final: 0.5916 (pm20) REVERT: B 202 LYS cc_start: 0.8703 (mttp) cc_final: 0.8127 (mttm) REVERT: B 237 ARG cc_start: 0.7868 (mtm180) cc_final: 0.6584 (mtm-85) REVERT: H 34 MET cc_start: 0.8860 (tpp) cc_final: 0.8638 (mmt) REVERT: H 159 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7864 (mt-10) REVERT: H 181 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7966 (tt) REVERT: H 186 LEU cc_start: 0.8404 (mp) cc_final: 0.7848 (mt) REVERT: L 11 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7924 (tt) REVERT: L 17 GLU cc_start: 0.8240 (tp30) cc_final: 0.7924 (tp30) REVERT: L 168 ASP cc_start: 0.7215 (t70) cc_final: 0.6963 (t0) outliers start: 22 outliers final: 18 residues processed: 125 average time/residue: 0.2035 time to fit residues: 33.4280 Evaluate side-chains 128 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 498 GLN 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 205 SER Chi-restraints excluded: chain B residue 227 VAL 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 181 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.147537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104758 restraints weight = 8312.463| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.49 r_work: 0.3036 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3317 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= 0.114 Angle : 0.567 9.163 9162 Z= 0.284 Chirality : 0.044 0.170 1023 Planarity : 0.005 0.085 1164 Dihedral : 5.281 49.979 950 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.03 % Allowed : 11.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.30), residues: 787 helix: -2.57 (0.74), residues: 32 sheet: -0.01 (0.33), residues: 275 loop : -1.73 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.014 0.002 HIS B 207 PHE 0.013 0.001 PHE B 238 TYR 0.014 0.001 TYR L 141 ARG 0.002 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 3.34021 ( 9) hydrogen bonds : bond 0.02674 ( 164) hydrogen bonds : angle 5.13899 ( 405) SS BOND : bond 0.00251 ( 10) SS BOND : angle 0.78574 ( 20) covalent geometry : bond 0.00267 ( 6720) covalent geometry : angle 0.55695 ( 9133) ********************** 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 135 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7673 (pm20) cc_final: 0.7412 (pt0) REVERT: A 386 LYS cc_start: 0.8185 (tppt) cc_final: 0.7341 (tttt) REVERT: A 586 ASP cc_start: 0.7950 (m-30) cc_final: 0.7637 (m-30) REVERT: B 101 ILE cc_start: 0.8621 (mm) cc_final: 0.8370 (mm) REVERT: B 134 GLN cc_start: 0.6588 (tp40) cc_final: 0.5907 (pm20) REVERT: B 202 LYS cc_start: 0.8699 (mttp) cc_final: 0.8090 (mtpm) REVERT: B 237 ARG cc_start: 0.7820 (mtm180) cc_final: 0.6570 (mtm-85) REVERT: H 159 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7867 (mt-10) REVERT: H 186 LEU cc_start: 0.8244 (mp) cc_final: 0.7905 (mt) REVERT: L 11 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7907 (tt) REVERT: L 17 GLU cc_start: 0.8215 (tp30) cc_final: 0.7904 (tp30) REVERT: L 168 ASP cc_start: 0.7238 (t70) cc_final: 0.6994 (t0) outliers start: 22 outliers final: 18 residues processed: 127 average time/residue: 0.2002 time to fit residues: 33.5477 Evaluate side-chains 130 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 498 GLN 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 205 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.148273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105465 restraints weight = 8363.965| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.49 r_work: 0.3033 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6733 Z= 0.108 Angle : 0.556 8.120 9162 Z= 0.279 Chirality : 0.044 0.170 1023 Planarity : 0.005 0.085 1164 Dihedral : 5.063 49.591 950 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.89 % Allowed : 11.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.30), residues: 787 helix: -2.47 (0.74), residues: 32 sheet: 0.04 (0.33), residues: 275 loop : -1.66 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.014 0.002 HIS B 207 PHE 0.013 0.001 PHE B 238 TYR 0.013 0.001 TYR L 141 ARG 0.002 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 3.07061 ( 9) hydrogen bonds : bond 0.02631 ( 164) hydrogen bonds : angle 5.05586 ( 405) SS BOND : bond 0.00227 ( 10) SS BOND : angle 0.78597 ( 20) covalent geometry : bond 0.00254 ( 6720) covalent geometry : angle 0.54687 ( 9133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4844.42 seconds wall clock time: 86 minutes 11.19 seconds (5171.19 seconds total)