Starting phenix.real_space_refine on Wed Jul 30 01:36:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqu_50669/07_2025/9fqu_50669_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqu_50669/07_2025/9fqu_50669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fqu_50669/07_2025/9fqu_50669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqu_50669/07_2025/9fqu_50669.map" model { file = "/net/cci-nas-00/data/ceres_data/9fqu_50669/07_2025/9fqu_50669_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqu_50669/07_2025/9fqu_50669_trim.cif" } resolution = 2.79 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= 0.051 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3948 2.51 5 N 956 2.21 5 O 1113 1.98 5 H 5785 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8277 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 22, 'TRANS': 523} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3331 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Unusual residues: {'NAG': 1, 'Y01': 2} Inner-chain residues flagged as termini: ['pdbres="ARG A1104 "'] Classifications: {'peptide': 1, 'undetermined': 3, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.72, per 1000 atoms: 0.57 Number of scatterers: 11844 At special positions: 0 Unit cell: (106.425, 81.675, 98.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 1113 8.00 N 956 7.00 C 3948 6.00 H 5785 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 132 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 218 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG D 1 " - " FUC D 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1101 " - " ASN A 229 " " NAG C 1 " - " ASN A 223 " " NAG D 1 " - " ASN B 46 " " NAG I 1 " - " ASN B 202 " Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 962.4 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 63.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.858A pdb=" N ALA A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 88 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 106 through 140 Processing helix chain 'A' and resid 142 through 152 Processing helix chain 'A' and resid 165 through 181 Processing helix chain 'A' and resid 186 through 212 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 243 through 260 removed outlier: 4.280A pdb=" N TYR A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 259 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.875A pdb=" N ALA A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 305 removed outlier: 3.820A pdb=" N VAL A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 327 through 349 removed outlier: 4.033A pdb=" N ALA A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 4.266A pdb=" N ARG A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.619A pdb=" N LYS A 370 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 Processing helix chain 'A' and resid 397 through 424 removed outlier: 3.546A pdb=" N ARG A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 482 through 509 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 518 through 542 removed outlier: 3.558A pdb=" N GLN A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.621A pdb=" N ALA B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 134 through 147 Processing helix chain 'B' and resid 161 through 168 removed outlier: 4.752A pdb=" N SER B 166 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 168 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 4.097A pdb=" N GLN B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 233 through 238 removed outlier: 4.081A pdb=" N THR B 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 67 removed outlier: 3.564A pdb=" N GLY B 151 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 197 through 201 373 hydrogen bonds defined for protein. 1071 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: 4.88 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5774 1.03 - 1.23: 26 1.23 - 1.42: 2562 1.42 - 1.62: 3582 1.62 - 1.82: 59 Bond restraints: 12003 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 MAN D 4 " pdb=" C2 MAN D 4 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C2 BMA D 3 " pdb=" C3 BMA D 3 " ideal model delta sigma weight residual 1.544 1.510 0.034 2.00e-02 2.50e+03 2.84e+00 ... (remaining 11998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 21122 1.44 - 2.87: 421 2.87 - 4.31: 52 4.31 - 5.74: 14 5.74 - 7.18: 4 Bond angle restraints: 21613 Sorted by residual: angle pdb=" C ARG A1104 " pdb=" CA ARG A1104 " pdb=" CB ARG A1104 " ideal model delta sigma weight residual 110.10 114.65 -4.55 1.90e+00 2.77e-01 5.75e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 105.77 7.18 3.00e+00 1.11e-01 5.72e+00 angle pdb=" C3 BMA I 3 " pdb=" C2 BMA I 3 " pdb=" O2 BMA I 3 " ideal model delta sigma weight residual 112.95 106.80 6.15 3.00e+00 1.11e-01 4.20e+00 angle pdb=" C3 MAN D 4 " pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 111.77 105.64 6.13 3.00e+00 1.11e-01 4.18e+00 angle pdb=" N ARG A1104 " pdb=" CA ARG A1104 " pdb=" C ARG A1104 " ideal model delta sigma weight residual 111.00 105.37 5.63 2.80e+00 1.28e-01 4.04e+00 ... (remaining 21608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 5617 21.64 - 43.28: 229 43.28 - 64.92: 107 64.92 - 86.56: 16 86.56 - 108.20: 8 Dihedral angle restraints: 5977 sinusoidal: 3319 harmonic: 2658 Sorted by residual: dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.49 108.20 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.54 106.16 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" CB CYS B 155 " pdb=" SG CYS B 155 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 123.50 -30.50 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 5974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 906 0.066 - 0.131: 103 0.131 - 0.197: 5 0.197 - 0.263: 1 0.263 - 0.329: 3 Chirality restraints: 1018 Sorted by residual: chirality pdb=" C1 NAG A1101 " pdb=" ND2 ASN A 229 " pdb=" C2 NAG A1101 " pdb=" O5 NAG A1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1015 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1104 " 0.637 9.50e-02 1.11e+02 3.68e-01 2.08e+03 pdb=" NE ARG A1104 " 0.124 2.00e-02 2.50e+03 pdb=" CZ ARG A1104 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A1104 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A1104 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG A1104 " -0.618 2.00e-02 2.50e+03 pdb="HH12 ARG A1104 " 0.624 2.00e-02 2.50e+03 pdb="HH21 ARG A1104 " 0.011 2.00e-02 2.50e+03 pdb="HH22 ARG A1104 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 102 " -0.013 2.00e-02 2.50e+03 9.15e-03 2.51e+00 pdb=" CG TYR A 102 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 102 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 102 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 102 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 102 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 102 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 102 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR A 102 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 102 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 56 " 0.125 9.50e-02 1.11e+02 4.20e-02 2.07e+00 pdb=" NE ARG B 56 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 56 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 56 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 56 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 56 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 56 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 56 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 56 " -0.001 2.00e-02 2.50e+03 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 991 2.23 - 2.82: 25851 2.82 - 3.42: 32695 3.42 - 4.01: 44195 4.01 - 4.60: 68824 Nonbonded interactions: 172556 Sorted by model distance: nonbonded pdb="HD22 ASN A 216 " pdb=" O LEU A 303 " model vdw 1.638 2.450 nonbonded pdb=" O TYR A 235 " pdb=" HH TYR A 307 " model vdw 1.657 2.450 nonbonded pdb=" O ASP B 195 " pdb=" HG1 THR B 226 " model vdw 1.680 2.450 nonbonded pdb=" O LEU A 337 " pdb=" HG SER A 341 " model vdw 1.683 2.450 nonbonded pdb=" HH TYR A 51 " pdb=" OD1 ASN A 197 " model vdw 1.685 2.450 ... (remaining 172551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.230 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.880 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:14.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.003 0.042 6235 Z= 0.151 Angle : 0.593 10.383 8546 Z= 0.270 Chirality : 0.042 0.329 1018 Planarity : 0.006 0.172 1030 Dihedral : 14.130 108.201 2426 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.32), residues: 761 helix: 2.01 (0.26), residues: 419 sheet: -0.22 (0.75), residues: 61 loop : 0.45 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 194 HIS 0.001 0.000 HIS B 239 PHE 0.010 0.001 PHE A 396 TYR 0.027 0.001 TYR A 102 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 4) link_NAG-ASN : angle 3.44171 ( 12) link_BETA1-4 : bond 0.01252 ( 5) link_BETA1-4 : angle 3.48993 ( 15) link_ALPHA1-3 : bond 0.00730 ( 1) link_ALPHA1-3 : angle 1.20201 ( 3) hydrogen bonds : bond 0.12982 ( 373) hydrogen bonds : angle 6.15742 ( 1071) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 1.30089 ( 3) SS BOND : bond 0.00193 ( 6) SS BOND : angle 0.51406 ( 12) covalent geometry : bond 0.00294 ( 6218) covalent geometry : angle 0.56001 ( 8501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.983 Fit side-chains REVERT: A 525 MET cc_start: 0.6903 (tpp) cc_final: 0.6341 (tpt) REVERT: A 599 TRP cc_start: 0.8334 (m100) cc_final: 0.7858 (m100) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 2.2282 time to fit residues: 216.2460 Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116189 restraints weight = 19184.792| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.14 r_work: 0.3242 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6235 Z= 0.139 Angle : 0.555 6.728 8546 Z= 0.277 Chirality : 0.040 0.270 1018 Planarity : 0.004 0.049 1030 Dihedral : 9.605 62.472 1180 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.16 % Allowed : 8.17 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.32), residues: 761 helix: 2.40 (0.26), residues: 418 sheet: 0.07 (0.83), residues: 55 loop : 0.46 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 540 HIS 0.004 0.001 HIS A 151 PHE 0.019 0.001 PHE A 87 TYR 0.009 0.001 TYR A 98 ARG 0.008 0.001 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 4) link_NAG-ASN : angle 2.89492 ( 12) link_BETA1-4 : bond 0.00847 ( 5) link_BETA1-4 : angle 2.44991 ( 15) link_ALPHA1-3 : bond 0.01072 ( 1) link_ALPHA1-3 : angle 2.97975 ( 3) hydrogen bonds : bond 0.04281 ( 373) hydrogen bonds : angle 4.68364 ( 1071) link_BETA1-6 : bond 0.00201 ( 1) link_BETA1-6 : angle 1.50909 ( 3) SS BOND : bond 0.00323 ( 6) SS BOND : angle 0.72446 ( 12) covalent geometry : bond 0.00303 ( 6218) covalent geometry : angle 0.53198 ( 8501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 525 MET cc_start: 0.6869 (tpp) cc_final: 0.6279 (tpt) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 1.9599 time to fit residues: 154.7327 Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 32 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113231 restraints weight = 19336.001| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.14 r_work: 0.3157 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6235 Z= 0.143 Angle : 0.529 6.149 8546 Z= 0.267 Chirality : 0.039 0.247 1018 Planarity : 0.004 0.058 1030 Dihedral : 7.365 58.136 1180 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.96 % Allowed : 8.97 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.32), residues: 761 helix: 2.35 (0.25), residues: 418 sheet: 0.15 (0.86), residues: 52 loop : 0.42 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 540 HIS 0.001 0.000 HIS B 89 PHE 0.017 0.002 PHE A 87 TYR 0.013 0.001 TYR B 240 ARG 0.004 0.001 ARG A1104 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 4) link_NAG-ASN : angle 2.56189 ( 12) link_BETA1-4 : bond 0.00769 ( 5) link_BETA1-4 : angle 2.08093 ( 15) link_ALPHA1-3 : bond 0.01168 ( 1) link_ALPHA1-3 : angle 2.53581 ( 3) hydrogen bonds : bond 0.04258 ( 373) hydrogen bonds : angle 4.49860 ( 1071) link_BETA1-6 : bond 0.00326 ( 1) link_BETA1-6 : angle 1.23893 ( 3) SS BOND : bond 0.00364 ( 6) SS BOND : angle 0.91864 ( 12) covalent geometry : bond 0.00317 ( 6218) covalent geometry : angle 0.51065 ( 8501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.8159 (m) cc_final: 0.7880 (t) REVERT: A 525 MET cc_start: 0.6976 (tpp) cc_final: 0.6354 (tpt) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 2.3697 time to fit residues: 188.1095 Evaluate side-chains 72 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114020 restraints weight = 19227.180| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.15 r_work: 0.3161 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6235 Z= 0.149 Angle : 0.525 5.845 8546 Z= 0.268 Chirality : 0.039 0.250 1018 Planarity : 0.004 0.062 1030 Dihedral : 6.572 57.284 1180 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.64 % Allowed : 9.78 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.31), residues: 761 helix: 2.28 (0.25), residues: 420 sheet: 0.05 (0.85), residues: 52 loop : 0.33 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 540 HIS 0.002 0.001 HIS B 89 PHE 0.021 0.002 PHE A 87 TYR 0.010 0.001 TYR A 98 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 4) link_NAG-ASN : angle 2.46981 ( 12) link_BETA1-4 : bond 0.00589 ( 5) link_BETA1-4 : angle 1.82196 ( 15) link_ALPHA1-3 : bond 0.01017 ( 1) link_ALPHA1-3 : angle 1.94342 ( 3) hydrogen bonds : bond 0.04013 ( 373) hydrogen bonds : angle 4.43786 ( 1071) link_BETA1-6 : bond 0.00300 ( 1) link_BETA1-6 : angle 1.25650 ( 3) SS BOND : bond 0.00364 ( 6) SS BOND : angle 0.88919 ( 12) covalent geometry : bond 0.00336 ( 6218) covalent geometry : angle 0.50977 ( 8501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.8150 (m) cc_final: 0.7890 (t) REVERT: A 483 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7893 (mtpt) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 1.8548 time to fit residues: 144.6109 Evaluate side-chains 71 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111404 restraints weight = 19256.724| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.14 r_work: 0.3100 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6235 Z= 0.149 Angle : 0.519 5.850 8546 Z= 0.265 Chirality : 0.038 0.232 1018 Planarity : 0.004 0.057 1030 Dihedral : 6.353 57.458 1180 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.80 % Allowed : 10.74 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.31), residues: 761 helix: 2.31 (0.25), residues: 421 sheet: -0.05 (0.84), residues: 52 loop : 0.26 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 136 HIS 0.003 0.001 HIS B 146 PHE 0.015 0.001 PHE A 87 TYR 0.011 0.001 TYR B 240 ARG 0.002 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 4) link_NAG-ASN : angle 2.31447 ( 12) link_BETA1-4 : bond 0.00698 ( 5) link_BETA1-4 : angle 1.72215 ( 15) link_ALPHA1-3 : bond 0.00959 ( 1) link_ALPHA1-3 : angle 1.64920 ( 3) hydrogen bonds : bond 0.04047 ( 373) hydrogen bonds : angle 4.42126 ( 1071) link_BETA1-6 : bond 0.00339 ( 1) link_BETA1-6 : angle 1.17954 ( 3) SS BOND : bond 0.00392 ( 6) SS BOND : angle 0.94746 ( 12) covalent geometry : bond 0.00338 ( 6218) covalent geometry : angle 0.50559 ( 8501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.8013 (m) cc_final: 0.7741 (t) REVERT: A 483 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7846 (mtpt) outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 1.8995 time to fit residues: 152.1202 Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113338 restraints weight = 19343.359| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.16 r_work: 0.3201 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6235 Z= 0.101 Angle : 0.487 5.723 8546 Z= 0.247 Chirality : 0.037 0.245 1018 Planarity : 0.004 0.063 1030 Dihedral : 6.072 59.016 1180 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.64 % Allowed : 10.58 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.25 (0.32), residues: 761 helix: 2.47 (0.25), residues: 427 sheet: -0.02 (0.86), residues: 52 loop : 0.33 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 136 HIS 0.003 0.001 HIS B 89 PHE 0.014 0.001 PHE A 87 TYR 0.009 0.001 TYR A 257 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 4) link_NAG-ASN : angle 2.21101 ( 12) link_BETA1-4 : bond 0.00678 ( 5) link_BETA1-4 : angle 1.66506 ( 15) link_ALPHA1-3 : bond 0.00926 ( 1) link_ALPHA1-3 : angle 1.39172 ( 3) hydrogen bonds : bond 0.03663 ( 373) hydrogen bonds : angle 4.26508 ( 1071) link_BETA1-6 : bond 0.00353 ( 1) link_BETA1-6 : angle 1.19327 ( 3) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.76346 ( 12) covalent geometry : bond 0.00211 ( 6218) covalent geometry : angle 0.47427 ( 8501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8086 (m) cc_final: 0.7868 (t) REVERT: A 146 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: A 525 MET cc_start: 0.7101 (tpp) cc_final: 0.6432 (tpt) REVERT: B 56 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7325 (mtt90) outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 2.5820 time to fit residues: 205.1058 Evaluate side-chains 69 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113462 restraints weight = 19420.077| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.15 r_work: 0.3130 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6235 Z= 0.107 Angle : 0.483 5.820 8546 Z= 0.245 Chirality : 0.037 0.230 1018 Planarity : 0.004 0.052 1030 Dihedral : 5.879 58.834 1180 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.64 % Allowed : 11.70 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.23 (0.32), residues: 761 helix: 2.46 (0.25), residues: 434 sheet: -0.12 (0.83), residues: 53 loop : 0.28 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 136 HIS 0.003 0.001 HIS B 89 PHE 0.012 0.001 PHE A 87 TYR 0.010 0.001 TYR A 257 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 4) link_NAG-ASN : angle 2.09546 ( 12) link_BETA1-4 : bond 0.00691 ( 5) link_BETA1-4 : angle 1.61889 ( 15) link_ALPHA1-3 : bond 0.00884 ( 1) link_ALPHA1-3 : angle 1.36290 ( 3) hydrogen bonds : bond 0.03660 ( 373) hydrogen bonds : angle 4.21050 ( 1071) link_BETA1-6 : bond 0.00386 ( 1) link_BETA1-6 : angle 1.18047 ( 3) SS BOND : bond 0.00300 ( 6) SS BOND : angle 0.71518 ( 12) covalent geometry : bond 0.00234 ( 6218) covalent geometry : angle 0.47099 ( 8501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.7978 (m) cc_final: 0.7743 (t) REVERT: A 146 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6521 (mm-30) REVERT: B 56 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7284 (mtt90) outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 1.6423 time to fit residues: 129.2012 Evaluate side-chains 72 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113447 restraints weight = 19326.251| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.14 r_work: 0.3163 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6235 Z= 0.108 Angle : 0.484 5.802 8546 Z= 0.245 Chirality : 0.037 0.238 1018 Planarity : 0.004 0.050 1030 Dihedral : 5.781 56.851 1180 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.48 % Allowed : 12.18 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.32), residues: 761 helix: 2.48 (0.25), residues: 434 sheet: -0.09 (0.83), residues: 53 loop : 0.29 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 136 HIS 0.003 0.001 HIS B 89 PHE 0.012 0.001 PHE A 87 TYR 0.009 0.001 TYR A 257 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 4) link_NAG-ASN : angle 2.09850 ( 12) link_BETA1-4 : bond 0.00686 ( 5) link_BETA1-4 : angle 1.58837 ( 15) link_ALPHA1-3 : bond 0.00840 ( 1) link_ALPHA1-3 : angle 1.30308 ( 3) hydrogen bonds : bond 0.03614 ( 373) hydrogen bonds : angle 4.16932 ( 1071) link_BETA1-6 : bond 0.00357 ( 1) link_BETA1-6 : angle 1.18976 ( 3) SS BOND : bond 0.00324 ( 6) SS BOND : angle 0.73381 ( 12) covalent geometry : bond 0.00235 ( 6218) covalent geometry : angle 0.47269 ( 8501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8045 (m) cc_final: 0.7825 (t) REVERT: A 146 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: B 56 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7329 (mtt90) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 1.6749 time to fit residues: 127.9655 Evaluate side-chains 69 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.149028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112911 restraints weight = 19270.072| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.14 r_work: 0.3170 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6235 Z= 0.120 Angle : 0.492 5.865 8546 Z= 0.249 Chirality : 0.037 0.225 1018 Planarity : 0.004 0.047 1030 Dihedral : 5.763 56.015 1180 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.80 % Allowed : 12.50 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.23 (0.32), residues: 761 helix: 2.46 (0.25), residues: 434 sheet: -0.15 (0.82), residues: 53 loop : 0.28 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 136 HIS 0.003 0.001 HIS B 89 PHE 0.012 0.001 PHE A 87 TYR 0.009 0.001 TYR A 257 ARG 0.006 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 4) link_NAG-ASN : angle 2.05382 ( 12) link_BETA1-4 : bond 0.00673 ( 5) link_BETA1-4 : angle 1.55619 ( 15) link_ALPHA1-3 : bond 0.00815 ( 1) link_ALPHA1-3 : angle 1.30602 ( 3) hydrogen bonds : bond 0.03681 ( 373) hydrogen bonds : angle 4.18070 ( 1071) link_BETA1-6 : bond 0.00351 ( 1) link_BETA1-6 : angle 1.19822 ( 3) SS BOND : bond 0.00351 ( 6) SS BOND : angle 0.80399 ( 12) covalent geometry : bond 0.00266 ( 6218) covalent geometry : angle 0.48088 ( 8501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8015 (m) cc_final: 0.7784 (t) REVERT: A 146 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6533 (mm-30) REVERT: B 56 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7369 (mtt90) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 1.7793 time to fit residues: 135.4120 Evaluate side-chains 70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 0.0270 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114280 restraints weight = 19194.754| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.13 r_work: 0.3158 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6235 Z= 0.098 Angle : 0.476 5.790 8546 Z= 0.240 Chirality : 0.037 0.243 1018 Planarity : 0.004 0.048 1030 Dihedral : 5.635 54.916 1180 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.32 % Allowed : 12.66 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.37 (0.32), residues: 761 helix: 2.59 (0.25), residues: 434 sheet: -0.13 (0.83), residues: 53 loop : 0.32 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 136 HIS 0.003 0.001 HIS B 89 PHE 0.011 0.001 PHE A 87 TYR 0.009 0.001 TYR A 257 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 4) link_NAG-ASN : angle 2.02673 ( 12) link_BETA1-4 : bond 0.00670 ( 5) link_BETA1-4 : angle 1.54601 ( 15) link_ALPHA1-3 : bond 0.00859 ( 1) link_ALPHA1-3 : angle 1.26769 ( 3) hydrogen bonds : bond 0.03504 ( 373) hydrogen bonds : angle 4.10778 ( 1071) link_BETA1-6 : bond 0.00375 ( 1) link_BETA1-6 : angle 1.16777 ( 3) SS BOND : bond 0.00310 ( 6) SS BOND : angle 0.70960 ( 12) covalent geometry : bond 0.00206 ( 6218) covalent geometry : angle 0.46497 ( 8501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.7991 (m) cc_final: 0.7778 (t) REVERT: A 146 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6550 (mm-30) REVERT: B 56 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7387 (mtt90) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 1.7583 time to fit residues: 126.3451 Evaluate side-chains 68 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112546 restraints weight = 19151.286| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.14 r_work: 0.3131 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6235 Z= 0.132 Angle : 0.498 5.872 8546 Z= 0.252 Chirality : 0.037 0.222 1018 Planarity : 0.004 0.048 1030 Dihedral : 5.708 56.132 1180 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.48 % Allowed : 12.82 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.32), residues: 761 helix: 2.55 (0.25), residues: 428 sheet: -0.12 (0.82), residues: 53 loop : 0.24 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 194 HIS 0.003 0.001 HIS B 89 PHE 0.012 0.001 PHE A 111 TYR 0.009 0.001 TYR A 257 ARG 0.005 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 4) link_NAG-ASN : angle 2.04141 ( 12) link_BETA1-4 : bond 0.00665 ( 5) link_BETA1-4 : angle 1.51798 ( 15) link_ALPHA1-3 : bond 0.00786 ( 1) link_ALPHA1-3 : angle 1.31211 ( 3) hydrogen bonds : bond 0.03716 ( 373) hydrogen bonds : angle 4.16699 ( 1071) link_BETA1-6 : bond 0.00358 ( 1) link_BETA1-6 : angle 1.19671 ( 3) SS BOND : bond 0.00358 ( 6) SS BOND : angle 0.81798 ( 12) covalent geometry : bond 0.00303 ( 6218) covalent geometry : angle 0.48729 ( 8501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8896.43 seconds wall clock time: 155 minutes 9.05 seconds (9309.05 seconds total)