Starting phenix.real_space_refine on Sun Apr 27 08:24:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez7_28729/04_2025/8ez7_28729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez7_28729/04_2025/8ez7_28729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez7_28729/04_2025/8ez7_28729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez7_28729/04_2025/8ez7_28729.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez7_28729/04_2025/8ez7_28729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez7_28729/04_2025/8ez7_28729.cif" } resolution = 2.6 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= -0.001 sd= 0.202 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 28 5.16 5 C 3065 2.51 5 N 845 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4927 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 372} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.82, per 1000 atoms: 0.78 Number of scatterers: 4927 At special positions: 0 Unit cell: (95.4, 83.74, 89.04, 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 28 16.00 O 989 8.00 N 845 7.00 C 3065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 614.5 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 4.8% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.744A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.585A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.547A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.784A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.788A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.412A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.976A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N LEU L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N SER L 65 " --> pdb=" O LEU L 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.090A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.648A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 124 removed outlier: 5.343A pdb=" N THR A 138 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ARG A 118 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN A 136 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 134 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL A 122 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 132 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N CYS A 124 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.276A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.733A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.637A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.321A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.561A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 429 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: 1.71 Time building geometry restraints manager: 1.55 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: 1609 1.34 - 1.46: 1256 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 5038 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.450 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 1.469 1.487 -0.018 1.28e-02 6.10e+03 2.03e+00 ... (remaining 5033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 6605 1.43 - 2.87: 191 2.87 - 4.30: 25 4.30 - 5.74: 7 5.74 - 7.17: 8 Bond angle restraints: 6836 Sorted by residual: angle pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 119.84 115.33 4.51 1.25e+00 6.40e-01 1.30e+01 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 113.47 -2.77 1.22e+00 6.72e-01 5.14e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 106.51 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sigma weight residual 113.65 110.51 3.14 1.47e+00 4.63e-01 4.56e+00 ... (remaining 6831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 2853 23.46 - 46.93: 196 46.93 - 70.39: 28 70.39 - 93.85: 15 93.85 - 117.31: 11 Dihedral angle restraints: 3103 sinusoidal: 1336 harmonic: 1767 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 134.03 -41.03 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA ALA A 177 " pdb=" C ALA A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C2 NAG A 503 " pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " pdb=" C5 NAG A 503 " ideal model delta sinusoidal sigma weight residual -62.96 54.35 -117.31 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 3100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 754 0.126 - 0.252: 5 0.252 - 0.378: 1 0.378 - 0.504: 0 0.504 - 0.630: 1 Chirality restraints: 761 Sorted by residual: chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 758 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.121 2.00e-02 2.50e+03 1.70e-01 3.63e+02 pdb=" CG ASN A 329 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.299 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO A 126 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO L 95 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.017 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 325 2.73 - 3.27: 4643 3.27 - 3.81: 8984 3.81 - 4.36: 11401 4.36 - 4.90: 19097 Nonbonded interactions: 44450 Sorted by model distance: nonbonded pdb=" OG SER A 179 " pdb=" OE2 GLU A 227 " model vdw 2.185 3.040 nonbonded pdb=" OG SER L 27A" pdb=" O ASP A 309 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP A 309 " pdb=" OG SER A 311 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 399 " pdb=" OG SER A 457 " model vdw 2.259 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.290 3.040 ... (remaining 44445 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=0.34 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: 2.830 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.270 Find NCS groups from input model: 0.060 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:16.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.004 0.085 5057 Z= 0.198 Angle : 0.733 23.370 6882 Z= 0.339 Chirality : 0.051 0.630 761 Planarity : 0.004 0.044 876 Dihedral : 18.250 117.313 1950 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.32 % Allowed : 16.76 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.34), residues: 618 helix: 0.60 (2.68), residues: 6 sheet: -0.05 (0.32), residues: 249 loop : 0.04 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd link_NAG-ASN : bond 0.02082 ( 4) link_NAG-ASN : angle 9.52468 ( 12) link_BETA1-4 : bond 0.00380 ( 2) link_BETA1-4 : angle 2.13839 ( 6) link_ALPHA1-2 : bond 0.00526 ( 1) link_ALPHA1-2 : angle 1.80415 ( 3) link_ALPHA1-3 : bond 0.00073 ( 1) link_ALPHA1-3 : angle 1.80432 ( 3) hydrogen bonds : bond 0.19115 ( 160) hydrogen bonds : angle 8.84799 ( 429) SS BOND : bond 0.00320 ( 11) SS BOND : angle 0.68859 ( 22) covalent geometry : bond 0.00414 ( 5038) covalent geometry : angle 0.61144 ( 6836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.578 Fit side-chains REVERT: A 277 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8125 (mt-10) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 1.5968 time to fit residues: 135.7124 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.138727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108881 restraints weight = 4742.282| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.36 r_work: 0.3026 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5057 Z= 0.144 Angle : 0.622 10.337 6882 Z= 0.317 Chirality : 0.049 0.421 761 Planarity : 0.004 0.042 876 Dihedral : 13.344 103.260 873 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.45 % Allowed : 16.01 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.33), residues: 618 helix: 0.26 (2.43), residues: 6 sheet: -0.08 (0.31), residues: 247 loop : -0.11 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.012 0.001 PHE A 354 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 4) link_NAG-ASN : angle 4.32611 ( 12) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 2.01435 ( 6) link_ALPHA1-2 : bond 0.00688 ( 1) link_ALPHA1-2 : angle 1.55582 ( 3) link_ALPHA1-3 : bond 0.00786 ( 1) link_ALPHA1-3 : angle 1.85319 ( 3) hydrogen bonds : bond 0.03774 ( 160) hydrogen bonds : angle 6.84466 ( 429) SS BOND : bond 0.00260 ( 11) SS BOND : angle 0.62156 ( 22) covalent geometry : bond 0.00311 ( 5038) covalent geometry : angle 0.59086 ( 6836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.576 Fit side-chains REVERT: H 38 ARG cc_start: 0.9077 (ptt180) cc_final: 0.8873 (ptt180) REVERT: L 100 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: A 277 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7986 (mt-10) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 1.3612 time to fit residues: 111.1551 Evaluate side-chains 76 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 0.0570 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110977 restraints weight = 4806.235| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.43 r_work: 0.3020 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5057 Z= 0.137 Angle : 0.592 11.250 6882 Z= 0.301 Chirality : 0.048 0.401 761 Planarity : 0.004 0.044 876 Dihedral : 10.309 99.043 867 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.39 % Allowed : 16.20 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.33), residues: 618 helix: 0.27 (2.35), residues: 6 sheet: 0.00 (0.32), residues: 232 loop : -0.14 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.001 TYR A 121 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00828 ( 4) link_NAG-ASN : angle 4.17097 ( 12) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 1.77416 ( 6) link_ALPHA1-2 : bond 0.00673 ( 1) link_ALPHA1-2 : angle 1.63563 ( 3) link_ALPHA1-3 : bond 0.01017 ( 1) link_ALPHA1-3 : angle 1.48332 ( 3) hydrogen bonds : bond 0.03514 ( 160) hydrogen bonds : angle 6.28939 ( 429) SS BOND : bond 0.00277 ( 11) SS BOND : angle 0.61043 ( 22) covalent geometry : bond 0.00296 ( 5038) covalent geometry : angle 0.56214 ( 6836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.639 Fit side-chains REVERT: H 38 ARG cc_start: 0.9069 (ptt180) cc_final: 0.8865 (ptt180) REVERT: A 277 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7974 (mt-10) outliers start: 18 outliers final: 8 residues processed: 86 average time/residue: 1.2404 time to fit residues: 111.7541 Evaluate side-chains 77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108998 restraints weight = 4851.363| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.40 r_work: 0.3013 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5057 Z= 0.173 Angle : 0.614 11.081 6882 Z= 0.315 Chirality : 0.049 0.413 761 Planarity : 0.004 0.044 876 Dihedral : 9.768 96.250 867 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.64 % Allowed : 16.76 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.33), residues: 618 helix: 0.20 (2.36), residues: 6 sheet: -0.03 (0.31), residues: 232 loop : -0.20 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.002 TYR A 121 ARG 0.001 0.000 ARG A 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00817 ( 4) link_NAG-ASN : angle 4.30724 ( 12) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 1.91888 ( 6) link_ALPHA1-2 : bond 0.00561 ( 1) link_ALPHA1-2 : angle 1.83928 ( 3) link_ALPHA1-3 : bond 0.00937 ( 1) link_ALPHA1-3 : angle 1.71567 ( 3) hydrogen bonds : bond 0.03506 ( 160) hydrogen bonds : angle 6.25200 ( 429) SS BOND : bond 0.00283 ( 11) SS BOND : angle 0.66683 ( 22) covalent geometry : bond 0.00383 ( 5038) covalent geometry : angle 0.58279 ( 6836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.631 Fit side-chains REVERT: H 38 ARG cc_start: 0.9075 (ptt180) cc_final: 0.8874 (ptt180) REVERT: L 100 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: A 277 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7992 (mt-10) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 1.5121 time to fit residues: 125.1280 Evaluate side-chains 79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.0000 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3543 r_free = 0.3543 target = 0.141646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112212 restraints weight = 4766.192| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.37 r_work: 0.3071 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5057 Z= 0.112 Angle : 0.563 10.625 6882 Z= 0.286 Chirality : 0.047 0.400 761 Planarity : 0.004 0.043 876 Dihedral : 8.959 92.551 867 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.77 % Allowed : 16.95 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.33), residues: 618 helix: 0.28 (2.35), residues: 6 sheet: 0.04 (0.31), residues: 237 loop : -0.20 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.012 0.001 PHE A 354 TYR 0.010 0.001 TYR A 121 ARG 0.001 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 4) link_NAG-ASN : angle 4.06853 ( 12) link_BETA1-4 : bond 0.00512 ( 2) link_BETA1-4 : angle 1.68227 ( 6) link_ALPHA1-2 : bond 0.00777 ( 1) link_ALPHA1-2 : angle 1.66905 ( 3) link_ALPHA1-3 : bond 0.01210 ( 1) link_ALPHA1-3 : angle 1.38379 ( 3) hydrogen bonds : bond 0.03009 ( 160) hydrogen bonds : angle 5.94646 ( 429) SS BOND : bond 0.00170 ( 11) SS BOND : angle 0.51316 ( 22) covalent geometry : bond 0.00238 ( 5038) covalent geometry : angle 0.53384 ( 6836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.490 Fit side-chains REVERT: L 100 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: A 277 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7997 (mt-10) REVERT: A 308 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8103 (mtmt) REVERT: A 337 CYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8424 (m) outliers start: 20 outliers final: 10 residues processed: 88 average time/residue: 1.5382 time to fit residues: 141.1638 Evaluate side-chains 82 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.112149 restraints weight = 4786.699| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.39 r_work: 0.3031 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5057 Z= 0.134 Angle : 0.580 10.571 6882 Z= 0.295 Chirality : 0.047 0.400 761 Planarity : 0.004 0.042 876 Dihedral : 8.733 90.198 867 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.82 % Allowed : 17.89 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.33), residues: 618 helix: 0.29 (2.36), residues: 6 sheet: 0.07 (0.31), residues: 237 loop : -0.17 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.001 TYR A 121 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 4) link_NAG-ASN : angle 4.11358 ( 12) link_BETA1-4 : bond 0.00429 ( 2) link_BETA1-4 : angle 1.80155 ( 6) link_ALPHA1-2 : bond 0.00652 ( 1) link_ALPHA1-2 : angle 1.78582 ( 3) link_ALPHA1-3 : bond 0.01020 ( 1) link_ALPHA1-3 : angle 1.47913 ( 3) hydrogen bonds : bond 0.03136 ( 160) hydrogen bonds : angle 5.94547 ( 429) SS BOND : bond 0.00242 ( 11) SS BOND : angle 0.73034 ( 22) covalent geometry : bond 0.00294 ( 5038) covalent geometry : angle 0.54968 ( 6836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.601 Fit side-chains REVERT: L 100 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: A 277 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8031 (mt-10) REVERT: A 308 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8085 (mtmt) REVERT: A 337 CYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8488 (m) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 1.1068 time to fit residues: 96.5163 Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3505 r_free = 0.3505 target = 0.138450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110533 restraints weight = 4783.117| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.40 r_work: 0.3013 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5057 Z= 0.162 Angle : 0.607 10.688 6882 Z= 0.309 Chirality : 0.048 0.394 761 Planarity : 0.004 0.042 876 Dihedral : 8.674 87.428 867 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.20 % Allowed : 17.89 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.33), residues: 618 helix: 0.27 (2.39), residues: 6 sheet: 0.08 (0.32), residues: 232 loop : -0.15 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 4) link_NAG-ASN : angle 4.16239 ( 12) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 1.89593 ( 6) link_ALPHA1-2 : bond 0.00584 ( 1) link_ALPHA1-2 : angle 1.88124 ( 3) link_ALPHA1-3 : bond 0.00917 ( 1) link_ALPHA1-3 : angle 1.51079 ( 3) hydrogen bonds : bond 0.03334 ( 160) hydrogen bonds : angle 5.99521 ( 429) SS BOND : bond 0.00253 ( 11) SS BOND : angle 0.81023 ( 22) covalent geometry : bond 0.00358 ( 5038) covalent geometry : angle 0.57682 ( 6836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.486 Fit side-chains REVERT: L 100 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: A 277 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7985 (mt-10) outliers start: 17 outliers final: 11 residues processed: 80 average time/residue: 1.2866 time to fit residues: 108.3967 Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3510 r_free = 0.3510 target = 0.138938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110779 restraints weight = 4805.820| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.42 r_work: 0.3010 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5057 Z= 0.160 Angle : 0.611 11.000 6882 Z= 0.311 Chirality : 0.048 0.381 761 Planarity : 0.004 0.042 876 Dihedral : 8.529 83.564 867 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.45 % Allowed : 18.27 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.33), residues: 618 helix: 0.25 (2.39), residues: 6 sheet: 0.05 (0.32), residues: 232 loop : -0.16 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.001 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 4) link_NAG-ASN : angle 4.15784 ( 12) link_BETA1-4 : bond 0.00429 ( 2) link_BETA1-4 : angle 1.89102 ( 6) link_ALPHA1-2 : bond 0.00596 ( 1) link_ALPHA1-2 : angle 1.87242 ( 3) link_ALPHA1-3 : bond 0.00948 ( 1) link_ALPHA1-3 : angle 1.49701 ( 3) hydrogen bonds : bond 0.03336 ( 160) hydrogen bonds : angle 5.98788 ( 429) SS BOND : bond 0.00275 ( 11) SS BOND : angle 1.04561 ( 22) covalent geometry : bond 0.00354 ( 5038) covalent geometry : angle 0.58016 ( 6836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.561 Fit side-chains REVERT: L 100 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: A 277 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7973 (mt-10) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 1.1629 time to fit residues: 94.9771 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111358 restraints weight = 4732.825| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.38 r_work: 0.3022 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5057 Z= 0.143 Angle : 0.600 11.403 6882 Z= 0.304 Chirality : 0.047 0.350 761 Planarity : 0.004 0.042 876 Dihedral : 8.099 75.047 867 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.82 % Allowed : 18.64 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.33), residues: 618 helix: 0.28 (2.38), residues: 6 sheet: 0.08 (0.32), residues: 232 loop : -0.16 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 4) link_NAG-ASN : angle 4.13336 ( 12) link_BETA1-4 : bond 0.00471 ( 2) link_BETA1-4 : angle 1.85866 ( 6) link_ALPHA1-2 : bond 0.00627 ( 1) link_ALPHA1-2 : angle 1.81555 ( 3) link_ALPHA1-3 : bond 0.00996 ( 1) link_ALPHA1-3 : angle 1.42665 ( 3) hydrogen bonds : bond 0.03243 ( 160) hydrogen bonds : angle 5.91201 ( 429) SS BOND : bond 0.00264 ( 11) SS BOND : angle 0.96258 ( 22) covalent geometry : bond 0.00314 ( 5038) covalent geometry : angle 0.56931 ( 6836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.579 Fit side-chains REVERT: L 100 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: A 277 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7956 (mt-10) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 1.1179 time to fit residues: 94.8536 Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 0.0170 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.141190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113603 restraints weight = 4789.420| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.41 r_work: 0.3050 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5057 Z= 0.120 Angle : 0.582 11.020 6882 Z= 0.294 Chirality : 0.045 0.253 761 Planarity : 0.004 0.042 876 Dihedral : 7.314 54.321 867 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.26 % Allowed : 19.02 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.33), residues: 618 helix: 0.34 (2.38), residues: 6 sheet: 0.09 (0.32), residues: 237 loop : -0.15 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.012 0.001 PHE A 354 TYR 0.011 0.001 TYR A 121 ARG 0.002 0.000 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 4) link_NAG-ASN : angle 4.23576 ( 12) link_BETA1-4 : bond 0.00501 ( 2) link_BETA1-4 : angle 1.76630 ( 6) link_ALPHA1-2 : bond 0.00688 ( 1) link_ALPHA1-2 : angle 1.76840 ( 3) link_ALPHA1-3 : bond 0.01074 ( 1) link_ALPHA1-3 : angle 1.33648 ( 3) hydrogen bonds : bond 0.03076 ( 160) hydrogen bonds : angle 5.81860 ( 429) SS BOND : bond 0.00194 ( 11) SS BOND : angle 0.81042 ( 22) covalent geometry : bond 0.00263 ( 5038) covalent geometry : angle 0.55030 ( 6836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.561 Fit side-chains REVERT: L 100 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: A 277 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7937 (mt-10) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 1.1017 time to fit residues: 95.6426 Evaluate side-chains 84 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.140079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108939 restraints weight = 4781.636| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.49 r_work: 0.3014 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5057 Z= 0.142 Angle : 0.590 11.619 6882 Z= 0.304 Chirality : 0.045 0.145 761 Planarity : 0.004 0.042 876 Dihedral : 6.914 52.740 867 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.64 % Allowed : 19.02 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.33), residues: 618 helix: 0.27 (2.37), residues: 6 sheet: 0.10 (0.32), residues: 237 loop : -0.13 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.001 PHE A 354 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 4) link_NAG-ASN : angle 4.25380 ( 12) link_BETA1-4 : bond 0.00453 ( 2) link_BETA1-4 : angle 1.88846 ( 6) link_ALPHA1-2 : bond 0.00619 ( 1) link_ALPHA1-2 : angle 1.87898 ( 3) link_ALPHA1-3 : bond 0.00862 ( 1) link_ALPHA1-3 : angle 1.39609 ( 3) hydrogen bonds : bond 0.03189 ( 160) hydrogen bonds : angle 5.85947 ( 429) SS BOND : bond 0.00260 ( 11) SS BOND : angle 0.91262 ( 22) covalent geometry : bond 0.00314 ( 5038) covalent geometry : angle 0.55742 ( 6836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5132.00 seconds wall clock time: 91 minutes 30.61 seconds (5490.61 seconds total)