Starting phenix.real_space_refine on Wed Sep 17 22:33:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqu_50669/09_2025/9fqu_50669_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqu_50669/09_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_50669/09_2025/9fqu_50669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqu_50669/09_2025/9fqu_50669.map" model { file = "/net/cci-nas-00/data/ceres_data/9fqu_50669/09_2025/9fqu_50669_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqu_50669/09_2025/9fqu_50669_trim.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'GLN:plan1': 1, '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: 1.95, per 1000 atoms: 0.16 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: 1.24 Conformation dependent library (CDL) restraints added in 411.9 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.19 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: 2.43 Time building geometry restraints manager: 1.62 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: 1.220 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG B 56 TYR 0.027 0.001 TYR A 102 PHE 0.010 0.001 PHE A 396 TRP 0.008 0.001 TRP B 194 HIS 0.001 0.000 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6218) covalent geometry : angle 0.56001 ( 8501) SS BOND : bond 0.00193 ( 6) SS BOND : angle 0.51406 ( 12) hydrogen bonds : bond 0.12982 ( 373) hydrogen bonds : angle 6.15742 ( 1071) link_ALPHA1-3 : bond 0.00730 ( 1) link_ALPHA1-3 : angle 1.20201 ( 3) link_BETA1-4 : bond 0.01252 ( 5) link_BETA1-4 : angle 3.48993 ( 15) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 1.30089 ( 3) link_NAG-ASN : bond 0.00545 ( 4) link_NAG-ASN : angle 3.44171 ( 12) *********************** 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 : 0.294 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: 1.0118 time to fit residues: 97.7923 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 : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.152720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116954 restraints weight = 19218.151| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.12 r_work: 0.3248 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1068 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= 0.133 Angle : 0.544 6.871 8546 Z= 0.272 Chirality : 0.039 0.268 1018 Planarity : 0.004 0.048 1030 Dihedral : 9.841 64.676 1180 Min Nonbonded Distance : 2.421 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.32), residues: 761 helix: 2.43 (0.26), residues: 418 sheet: 0.06 (0.82), residues: 55 loop : 0.47 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1104 TYR 0.008 0.001 TYR A 98 PHE 0.018 0.001 PHE A 87 TRP 0.006 0.001 TRP A 540 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6218) covalent geometry : angle 0.52032 ( 8501) SS BOND : bond 0.00314 ( 6) SS BOND : angle 0.68597 ( 12) hydrogen bonds : bond 0.04368 ( 373) hydrogen bonds : angle 4.70480 ( 1071) link_ALPHA1-3 : bond 0.00995 ( 1) link_ALPHA1-3 : angle 2.79482 ( 3) link_BETA1-4 : bond 0.00787 ( 5) link_BETA1-4 : angle 2.43796 ( 15) link_BETA1-6 : bond 0.00199 ( 1) link_BETA1-6 : angle 1.38764 ( 3) link_NAG-ASN : bond 0.00526 ( 4) link_NAG-ASN : angle 2.92293 ( 12) *********************** 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 76 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 525 MET cc_start: 0.6895 (tpp) cc_final: 0.6292 (tpt) REVERT: A 599 TRP cc_start: 0.8310 (m100) cc_final: 0.7857 (m100) REVERT: B 188 TRP cc_start: 0.6930 (p90) cc_final: 0.6694 (p90) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.9276 time to fit residues: 73.8433 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111996 restraints weight = 19558.931| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.15 r_work: 0.3109 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6235 Z= 0.169 Angle : 0.552 6.252 8546 Z= 0.279 Chirality : 0.040 0.256 1018 Planarity : 0.004 0.055 1030 Dihedral : 7.839 59.751 1180 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.64 % Allowed : 9.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.32), residues: 761 helix: 2.25 (0.25), residues: 418 sheet: 0.18 (0.85), residues: 52 loop : 0.39 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1104 TYR 0.013 0.001 TYR B 240 PHE 0.019 0.002 PHE A 87 TRP 0.008 0.001 TRP A 540 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6218) covalent geometry : angle 0.53242 ( 8501) SS BOND : bond 0.00423 ( 6) SS BOND : angle 0.98726 ( 12) hydrogen bonds : bond 0.04462 ( 373) hydrogen bonds : angle 4.58746 ( 1071) link_ALPHA1-3 : bond 0.01100 ( 1) link_ALPHA1-3 : angle 2.74012 ( 3) link_BETA1-4 : bond 0.00704 ( 5) link_BETA1-4 : angle 2.12406 ( 15) link_BETA1-6 : bond 0.00263 ( 1) link_BETA1-6 : angle 1.31742 ( 3) link_NAG-ASN : bond 0.00529 ( 4) link_NAG-ASN : angle 2.66521 ( 12) *********************** 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 72 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 525 MET cc_start: 0.6941 (tpp) cc_final: 0.6322 (tpt) outliers start: 4 outliers final: 0 residues processed: 71 average time/residue: 0.9013 time to fit residues: 68.1254 Evaluate side-chains 69 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.149422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113037 restraints weight = 19344.686| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.15 r_work: 0.3139 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1714 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= 0.122 Angle : 0.509 5.988 8546 Z= 0.257 Chirality : 0.038 0.250 1018 Planarity : 0.004 0.068 1030 Dihedral : 6.724 59.260 1180 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.80 % Allowed : 9.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.32), residues: 761 helix: 2.35 (0.25), residues: 420 sheet: 0.12 (0.86), residues: 52 loop : 0.36 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.009 0.001 TYR A 98 PHE 0.019 0.001 PHE A 87 TRP 0.007 0.001 TRP B 136 HIS 0.002 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6218) covalent geometry : angle 0.49227 ( 8501) SS BOND : bond 0.00333 ( 6) SS BOND : angle 0.84588 ( 12) hydrogen bonds : bond 0.03920 ( 373) hydrogen bonds : angle 4.41838 ( 1071) link_ALPHA1-3 : bond 0.01032 ( 1) link_ALPHA1-3 : angle 2.05351 ( 3) link_BETA1-4 : bond 0.00708 ( 5) link_BETA1-4 : angle 1.91871 ( 15) link_BETA1-6 : bond 0.00332 ( 1) link_BETA1-6 : angle 1.20863 ( 3) link_NAG-ASN : bond 0.00458 ( 4) link_NAG-ASN : angle 2.44471 ( 12) *********************** 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 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.8111 (m) cc_final: 0.7858 (t) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.8753 time to fit residues: 70.7980 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 : 0.179 ------------------------------------------------------------------------------- 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 114 SER 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 51 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111465 restraints weight = 19379.907| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.15 r_work: 0.3111 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6235 Z= 0.158 Angle : 0.528 5.934 8546 Z= 0.269 Chirality : 0.038 0.237 1018 Planarity : 0.004 0.057 1030 Dihedral : 6.437 55.915 1180 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.12 % Allowed : 10.26 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.32), residues: 761 helix: 2.28 (0.25), residues: 421 sheet: -0.06 (0.84), residues: 52 loop : 0.32 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.011 0.001 TYR B 240 PHE 0.019 0.002 PHE A 147 TRP 0.007 0.001 TRP B 136 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6218) covalent geometry : angle 0.51375 ( 8501) SS BOND : bond 0.00405 ( 6) SS BOND : angle 0.95293 ( 12) hydrogen bonds : bond 0.04099 ( 373) hydrogen bonds : angle 4.44238 ( 1071) link_ALPHA1-3 : bond 0.00991 ( 1) link_ALPHA1-3 : angle 1.74712 ( 3) link_BETA1-4 : bond 0.00679 ( 5) link_BETA1-4 : angle 1.73973 ( 15) link_BETA1-6 : bond 0.00326 ( 1) link_BETA1-6 : angle 1.21481 ( 3) link_NAG-ASN : bond 0.00485 ( 4) link_NAG-ASN : angle 2.37122 ( 12) *********************** 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 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.8067 (m) cc_final: 0.7795 (t) REVERT: A 483 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7855 (mtpt) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.8689 time to fit residues: 70.2472 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 : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.149292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113054 restraints weight = 19378.112| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.16 r_work: 0.3155 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6235 Z= 0.108 Angle : 0.492 5.787 8546 Z= 0.249 Chirality : 0.037 0.245 1018 Planarity : 0.004 0.062 1030 Dihedral : 6.149 58.046 1180 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.64 % Allowed : 10.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.32), residues: 761 helix: 2.49 (0.25), residues: 421 sheet: 0.01 (0.85), residues: 52 loop : 0.30 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.009 0.001 TYR A 257 PHE 0.016 0.001 PHE A 87 TRP 0.008 0.001 TRP B 136 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6218) covalent geometry : angle 0.47855 ( 8501) SS BOND : bond 0.00313 ( 6) SS BOND : angle 0.80382 ( 12) hydrogen bonds : bond 0.03743 ( 373) hydrogen bonds : angle 4.30666 ( 1071) link_ALPHA1-3 : bond 0.00912 ( 1) link_ALPHA1-3 : angle 1.46770 ( 3) link_BETA1-4 : bond 0.00718 ( 5) link_BETA1-4 : angle 1.69288 ( 15) link_BETA1-6 : bond 0.00338 ( 1) link_BETA1-6 : angle 1.17365 ( 3) link_NAG-ASN : bond 0.00445 ( 4) link_NAG-ASN : angle 2.24339 ( 12) *********************** 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 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.8062 (m) cc_final: 0.7842 (t) REVERT: A 525 MET cc_start: 0.7057 (tpp) cc_final: 0.6410 (tpt) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.8565 time to fit residues: 64.5786 Evaluate side-chains 70 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.148158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111985 restraints weight = 19363.067| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.15 r_work: 0.3123 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2014 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= 0.136 Angle : 0.505 5.874 8546 Z= 0.257 Chirality : 0.038 0.233 1018 Planarity : 0.004 0.059 1030 Dihedral : 6.064 59.150 1180 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.80 % Allowed : 11.22 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.32), residues: 761 helix: 2.46 (0.25), residues: 421 sheet: -0.08 (0.84), residues: 52 loop : 0.33 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 56 TYR 0.010 0.001 TYR A 257 PHE 0.019 0.001 PHE A 147 TRP 0.007 0.001 TRP B 136 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6218) covalent geometry : angle 0.49259 ( 8501) SS BOND : bond 0.00371 ( 6) SS BOND : angle 0.86401 ( 12) hydrogen bonds : bond 0.03862 ( 373) hydrogen bonds : angle 4.30930 ( 1071) link_ALPHA1-3 : bond 0.00870 ( 1) link_ALPHA1-3 : angle 1.43821 ( 3) link_BETA1-4 : bond 0.00672 ( 5) link_BETA1-4 : angle 1.64313 ( 15) link_BETA1-6 : bond 0.00357 ( 1) link_BETA1-6 : angle 1.20710 ( 3) link_NAG-ASN : bond 0.00465 ( 4) link_NAG-ASN : angle 2.20648 ( 12) *********************** 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 76 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.7983 (m) cc_final: 0.7738 (t) REVERT: A 483 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7834 (mtpt) REVERT: B 56 ARG cc_start: 0.7521 (mtt90) cc_final: 0.7263 (mtt90) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.8140 time to fit residues: 65.3543 Evaluate side-chains 72 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 114 SER 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 55 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.145486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108906 restraints weight = 19264.755| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.17 r_work: 0.3086 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6235 Z= 0.199 Angle : 0.555 5.958 8546 Z= 0.285 Chirality : 0.039 0.228 1018 Planarity : 0.004 0.052 1030 Dihedral : 6.292 57.280 1180 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.96 % Allowed : 11.54 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.31), residues: 761 helix: 2.15 (0.25), residues: 421 sheet: -0.12 (0.80), residues: 53 loop : 0.27 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.010 0.001 TYR A 257 PHE 0.019 0.002 PHE A 147 TRP 0.007 0.001 TRP B 217 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 6218) covalent geometry : angle 0.54173 ( 8501) SS BOND : bond 0.00524 ( 6) SS BOND : angle 1.16263 ( 12) hydrogen bonds : bond 0.04264 ( 373) hydrogen bonds : angle 4.45584 ( 1071) link_ALPHA1-3 : bond 0.00845 ( 1) link_ALPHA1-3 : angle 1.53620 ( 3) link_BETA1-4 : bond 0.00653 ( 5) link_BETA1-4 : angle 1.61104 ( 15) link_BETA1-6 : bond 0.00335 ( 1) link_BETA1-6 : angle 1.23133 ( 3) link_NAG-ASN : bond 0.00574 ( 4) link_NAG-ASN : angle 2.39622 ( 12) *********************** 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 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.301 Fit side-chains REVERT: A 44 SER cc_start: 0.8044 (m) cc_final: 0.7782 (t) REVERT: A 483 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7873 (mtpt) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.9008 time to fit residues: 69.1703 Evaluate side-chains 71 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 114 SER 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 62 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.0170 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.2554 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.151217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115091 restraints weight = 19028.433| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.15 r_work: 0.3142 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2154 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= 0.096 Angle : 0.488 5.713 8546 Z= 0.248 Chirality : 0.037 0.242 1018 Planarity : 0.004 0.069 1030 Dihedral : 5.946 56.787 1180 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.64 % Allowed : 12.18 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.32), residues: 761 helix: 2.49 (0.25), residues: 427 sheet: -0.03 (0.86), residues: 52 loop : 0.31 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 56 TYR 0.010 0.001 TYR A 257 PHE 0.017 0.001 PHE A 147 TRP 0.010 0.001 TRP B 136 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 6218) covalent geometry : angle 0.47616 ( 8501) SS BOND : bond 0.00315 ( 6) SS BOND : angle 0.77107 ( 12) hydrogen bonds : bond 0.03624 ( 373) hydrogen bonds : angle 4.22451 ( 1071) link_ALPHA1-3 : bond 0.00884 ( 1) link_ALPHA1-3 : angle 1.20667 ( 3) link_BETA1-4 : bond 0.00702 ( 5) link_BETA1-4 : angle 1.61500 ( 15) link_BETA1-6 : bond 0.00385 ( 1) link_BETA1-6 : angle 1.14869 ( 3) link_NAG-ASN : bond 0.00434 ( 4) link_NAG-ASN : angle 2.12735 ( 12) *********************** 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 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.7939 (m) cc_final: 0.7722 (t) REVERT: A 146 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6481 (mm-30) REVERT: A 525 MET cc_start: 0.6944 (tpp) cc_final: 0.6262 (tpt) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.8544 time to fit residues: 66.7872 Evaluate side-chains 71 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain B residue 189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.148209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112005 restraints weight = 19428.797| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.15 r_work: 0.3124 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2241 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= 0.127 Angle : 0.503 5.872 8546 Z= 0.255 Chirality : 0.037 0.230 1018 Planarity : 0.004 0.049 1030 Dihedral : 5.853 56.902 1180 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.48 % Allowed : 12.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.32), residues: 761 helix: 2.55 (0.25), residues: 421 sheet: -0.16 (0.81), residues: 53 loop : 0.29 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.017 0.001 TYR B 240 PHE 0.011 0.001 PHE A 111 TRP 0.009 0.001 TRP B 69 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6218) covalent geometry : angle 0.49096 ( 8501) SS BOND : bond 0.00375 ( 6) SS BOND : angle 0.83848 ( 12) hydrogen bonds : bond 0.03767 ( 373) hydrogen bonds : angle 4.24458 ( 1071) link_ALPHA1-3 : bond 0.00815 ( 1) link_ALPHA1-3 : angle 1.31801 ( 3) link_BETA1-4 : bond 0.00684 ( 5) link_BETA1-4 : angle 1.57187 ( 15) link_BETA1-6 : bond 0.00336 ( 1) link_BETA1-6 : angle 1.19949 ( 3) link_NAG-ASN : bond 0.00431 ( 4) link_NAG-ASN : angle 2.11786 ( 12) ********************** 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 72 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.306 Fit side-chains REVERT: A 44 SER cc_start: 0.7977 (m) cc_final: 0.7741 (t) REVERT: A 146 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6463 (mm-30) REVERT: A 525 MET cc_start: 0.6962 (tpp) cc_final: 0.6270 (tpt) outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.8358 time to fit residues: 63.3362 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 : 0.217 ------------------------------------------------------------------------------- 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 114 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.148974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112922 restraints weight = 19381.085| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.15 r_work: 0.3135 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2248 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= 0.114 Angle : 0.491 5.828 8546 Z= 0.249 Chirality : 0.037 0.239 1018 Planarity : 0.003 0.049 1030 Dihedral : 5.808 58.299 1180 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.48 % Allowed : 12.66 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.32), residues: 761 helix: 2.61 (0.25), residues: 421 sheet: -0.06 (0.84), residues: 53 loop : 0.31 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 424 TYR 0.010 0.001 TYR A 257 PHE 0.011 0.001 PHE A 87 TRP 0.012 0.001 TRP B 69 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6218) covalent geometry : angle 0.47980 ( 8501) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.79718 ( 12) hydrogen bonds : bond 0.03678 ( 373) hydrogen bonds : angle 4.20002 ( 1071) link_ALPHA1-3 : bond 0.00785 ( 1) link_ALPHA1-3 : angle 1.23576 ( 3) link_BETA1-4 : bond 0.00693 ( 5) link_BETA1-4 : angle 1.56729 ( 15) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.19715 ( 3) link_NAG-ASN : bond 0.00434 ( 4) link_NAG-ASN : angle 2.09846 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4218.05 seconds wall clock time: 72 minutes 2.77 seconds (4322.77 seconds total)