Starting phenix.real_space_refine on Fri Aug 22 17:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wre_37775/08_2025/8wre_37775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wre_37775/08_2025/8wre_37775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wre_37775/08_2025/8wre_37775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wre_37775/08_2025/8wre_37775.map" model { file = "/net/cci-nas-00/data/ceres_data/8wre_37775/08_2025/8wre_37775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wre_37775/08_2025/8wre_37775.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4081 2.51 5 N 1017 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6328 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2948 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "L" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "H" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1702 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.24 Number of scatterers: 6328 At special positions: 0 Unit cell: (76.56, 80.96, 134.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1188 8.00 N 1017 7.00 C 4081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 206 " 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 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 378.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1526 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 46.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.543A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 126 through 157 removed outlier: 4.936A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.791A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 Processing helix chain 'A' and resid 182 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.939A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.747A pdb=" N GLU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.859A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.534A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.580A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.746A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 4.387A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 447 removed outlier: 3.672A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.530A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.024A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.698A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.736A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.931A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.597A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.771A pdb=" N SER H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.017A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.692A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA4, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.063A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.626A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.033A pdb=" N PHE H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP H 100 " --> pdb=" O MET H 111 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N MET H 111 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.790A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.790A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.901A pdb=" N ILE H 204 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR H 215 " --> pdb=" O HIS H 210 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1947 1.34 - 1.46: 1567 1.46 - 1.58: 2899 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 6480 Sorted by residual: bond pdb=" CB PHE A 166 " pdb=" CG PHE A 166 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.09e+00 bond pdb=" C3 LDP A 601 " pdb=" O1 LDP A 601 " ideal model delta sigma weight residual 1.353 1.373 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C4 LDP A 601 " pdb=" O2 LDP A 601 " ideal model delta sigma weight residual 1.355 1.373 -0.018 2.00e-02 2.50e+03 7.94e-01 bond pdb=" C PRO A 236 " pdb=" N PRO A 237 " ideal model delta sigma weight residual 1.335 1.347 -0.011 1.36e-02 5.41e+03 6.72e-01 bond pdb=" CG PRO L 95 " pdb=" CD PRO L 95 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.29e-01 ... (remaining 6475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8587 1.34 - 2.67: 165 2.67 - 4.01: 45 4.01 - 5.34: 18 5.34 - 6.68: 3 Bond angle restraints: 8818 Sorted by residual: angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.18 114.72 -4.54 1.56e+00 4.11e-01 8.47e+00 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 115.50 -5.69 2.21e+00 2.05e-01 6.63e+00 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.34 117.04 -4.70 2.04e+00 2.40e-01 5.31e+00 angle pdb=" C ILE H 48 " pdb=" N GLY H 49 " pdb=" CA GLY H 49 " ideal model delta sigma weight residual 121.03 117.57 3.46 1.51e+00 4.39e-01 5.24e+00 angle pdb=" C ALA A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta sigma weight residual 123.17 120.00 3.17 1.49e+00 4.50e-01 4.53e+00 ... (remaining 8813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3516 16.42 - 32.83: 262 32.83 - 49.25: 46 49.25 - 65.67: 9 65.67 - 82.09: 3 Dihedral angle restraints: 3836 sinusoidal: 1450 harmonic: 2386 Sorted by residual: dihedral pdb=" CA GLN L 6 " pdb=" C GLN L 6 " pdb=" N SER L 7 " pdb=" CA SER L 7 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 61.41 31.59 1 1.00e+01 1.00e-02 1.42e+01 dihedral pdb=" CA ASP L 143 " pdb=" CB ASP L 143 " pdb=" CG ASP L 143 " pdb=" OD1 ASP L 143 " ideal model delta sinusoidal sigma weight residual -30.00 -89.27 59.27 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 3833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 601 0.029 - 0.058: 256 0.058 - 0.087: 97 0.087 - 0.116: 51 0.116 - 0.145: 12 Chirality restraints: 1017 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1014 not shown) Planarity restraints: 1102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 161 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 236 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 166 " -0.016 2.00e-02 2.50e+03 1.04e-02 1.90e+00 pdb=" CG PHE A 166 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 166 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 166 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 166 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 166 " -0.010 2.00e-02 2.50e+03 ... (remaining 1099 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1425 2.79 - 3.32: 5770 3.32 - 3.85: 10194 3.85 - 4.37: 11691 4.37 - 4.90: 21692 Nonbonded interactions: 50772 Sorted by model distance: nonbonded pdb=" OE1 GLU A 216 " pdb=" OG1 THR L 31 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR H 195 " pdb=" OG1 THR H 198 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP L 151 " pdb=" OG SER L 191 " model vdw 2.311 3.040 nonbonded pdb=" O LEU A 342 " pdb=" ND2 ASN A 346 " model vdw 2.369 3.120 nonbonded pdb=" O LEU A 133 " pdb=" OG SER A 137 " model vdw 2.385 3.040 ... (remaining 50767 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 0.034 6484 Z= 0.130 Angle : 0.543 6.680 8826 Z= 0.278 Chirality : 0.042 0.145 1017 Planarity : 0.004 0.043 1102 Dihedral : 12.085 82.085 2298 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.24 (0.30), residues: 821 helix: 1.76 (0.29), residues: 330 sheet: 1.24 (0.35), residues: 219 loop : -0.69 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.013 0.001 TYR A 433 PHE 0.019 0.001 PHE A 166 TRP 0.009 0.001 TRP H 114 HIS 0.002 0.000 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6480) covalent geometry : angle 0.54249 ( 8818) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.90320 ( 8) hydrogen bonds : bond 0.13501 ( 363) hydrogen bonds : angle 6.23849 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.279 Fit side-chains REVERT: A 324 CYS cc_start: 0.8016 (m) cc_final: 0.7811 (m) REVERT: A 433 TYR cc_start: 0.8474 (m-80) cc_final: 0.8260 (m-80) outliers start: 0 outliers final: 1 residues processed: 91 average time/residue: 0.6333 time to fit residues: 60.2914 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 157 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN L 190 ASN L 210 ASN H 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.086426 restraints weight = 9034.384| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.12 r_work: 0.2887 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6484 Z= 0.121 Angle : 0.550 9.973 8826 Z= 0.281 Chirality : 0.042 0.171 1017 Planarity : 0.004 0.043 1102 Dihedral : 4.427 50.276 887 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.14 % Allowed : 5.84 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.52 (0.30), residues: 821 helix: 1.92 (0.30), residues: 335 sheet: 1.51 (0.35), residues: 216 loop : -0.58 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.011 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.007 0.001 TRP H 114 HIS 0.002 0.001 HIS H 210 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6480) covalent geometry : angle 0.54995 ( 8818) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.67860 ( 8) hydrogen bonds : bond 0.03775 ( 363) hydrogen bonds : angle 4.81049 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.215 Fit side-chains REVERT: A 433 TYR cc_start: 0.8801 (m-80) cc_final: 0.8539 (m-80) outliers start: 8 outliers final: 3 residues processed: 91 average time/residue: 0.6164 time to fit residues: 58.6136 Evaluate side-chains 81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain L residue 157 ASN Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN L 28 ASN L 190 ASN L 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.085836 restraints weight = 8963.095| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.12 r_work: 0.2878 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6484 Z= 0.123 Angle : 0.545 10.152 8826 Z= 0.276 Chirality : 0.042 0.168 1017 Planarity : 0.005 0.047 1102 Dihedral : 4.317 46.670 887 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.85 % Allowed : 9.12 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.58 (0.30), residues: 821 helix: 1.99 (0.30), residues: 335 sheet: 1.49 (0.35), residues: 219 loop : -0.57 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 274 TYR 0.012 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6480) covalent geometry : angle 0.54501 ( 8818) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.67372 ( 8) hydrogen bonds : bond 0.03703 ( 363) hydrogen bonds : angle 4.60638 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.262 Fit side-chains REVERT: A 278 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: A 433 TYR cc_start: 0.8794 (m-80) cc_final: 0.8541 (m-80) REVERT: L 18 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7824 (ttm110) REVERT: L 156 GLN cc_start: 0.8038 (mp10) cc_final: 0.7812 (mp10) outliers start: 13 outliers final: 5 residues processed: 78 average time/residue: 0.6103 time to fit residues: 49.9210 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.082019 restraints weight = 9184.077| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.15 r_work: 0.2809 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6484 Z= 0.196 Angle : 0.601 9.246 8826 Z= 0.306 Chirality : 0.044 0.159 1017 Planarity : 0.005 0.046 1102 Dihedral : 4.446 40.809 885 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.85 % Allowed : 11.25 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.40 (0.30), residues: 821 helix: 1.79 (0.30), residues: 336 sheet: 1.41 (0.35), residues: 213 loop : -0.55 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 274 TYR 0.016 0.002 TYR A 422 PHE 0.019 0.002 PHE A 238 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 6480) covalent geometry : angle 0.60006 ( 8818) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.35516 ( 8) hydrogen bonds : bond 0.04660 ( 363) hydrogen bonds : angle 4.73989 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.261 Fit side-chains REVERT: A 34 ASN cc_start: 0.8550 (m-40) cc_final: 0.8342 (m110) REVERT: A 433 TYR cc_start: 0.8843 (m-80) cc_final: 0.8611 (m-80) REVERT: L 145 ASN cc_start: 0.7789 (t0) cc_final: 0.7275 (t0) REVERT: L 156 GLN cc_start: 0.8074 (mp10) cc_final: 0.7843 (mp10) REVERT: H 89 ASP cc_start: 0.8846 (t70) cc_final: 0.8443 (t0) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.5936 time to fit residues: 52.2208 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 65 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN L 190 ASN L 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.083351 restraints weight = 9160.820| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.14 r_work: 0.2836 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6484 Z= 0.144 Angle : 0.566 9.966 8826 Z= 0.287 Chirality : 0.043 0.178 1017 Planarity : 0.005 0.045 1102 Dihedral : 4.338 38.760 885 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.71 % Allowed : 12.25 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.43 (0.30), residues: 821 helix: 1.90 (0.30), residues: 336 sheet: 1.29 (0.34), residues: 216 loop : -0.55 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 274 TYR 0.013 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6480) covalent geometry : angle 0.56406 ( 8818) SS BOND : bond 0.00444 ( 4) SS BOND : angle 1.81865 ( 8) hydrogen bonds : bond 0.04062 ( 363) hydrogen bonds : angle 4.62149 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.261 Fit side-chains REVERT: A 34 ASN cc_start: 0.8470 (m-40) cc_final: 0.8268 (m110) REVERT: A 433 TYR cc_start: 0.8811 (m-80) cc_final: 0.8582 (m-80) REVERT: L 145 ASN cc_start: 0.7728 (t0) cc_final: 0.7238 (t0) REVERT: L 156 GLN cc_start: 0.8032 (mp10) cc_final: 0.7758 (mp10) REVERT: L 169 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8331 (tttp) REVERT: H 89 ASP cc_start: 0.8884 (t70) cc_final: 0.8490 (t0) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.6148 time to fit residues: 54.1079 Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 65 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 0.0060 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 overall best weight: 0.4432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.085763 restraints weight = 9093.208| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.10 r_work: 0.2880 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6484 Z= 0.111 Angle : 0.534 9.791 8826 Z= 0.269 Chirality : 0.041 0.183 1017 Planarity : 0.005 0.057 1102 Dihedral : 4.175 37.493 885 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.14 % Allowed : 12.68 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.57 (0.30), residues: 821 helix: 2.08 (0.30), residues: 336 sheet: 1.33 (0.34), residues: 216 loop : -0.55 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 274 TYR 0.010 0.001 TYR A 422 PHE 0.014 0.001 PHE A 238 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6480) covalent geometry : angle 0.53171 ( 8818) SS BOND : bond 0.00512 ( 4) SS BOND : angle 1.76493 ( 8) hydrogen bonds : bond 0.03462 ( 363) hydrogen bonds : angle 4.45805 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.354 Fit side-chains REVERT: A 17 ARG cc_start: 0.8520 (mpt-90) cc_final: 0.8301 (mmt-90) REVERT: A 433 TYR cc_start: 0.8805 (m-80) cc_final: 0.8557 (m-80) REVERT: L 145 ASN cc_start: 0.7684 (t0) cc_final: 0.7201 (t0) REVERT: L 156 GLN cc_start: 0.8024 (mp10) cc_final: 0.7746 (mp10) REVERT: L 169 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8364 (tttp) REVERT: H 89 ASP cc_start: 0.8907 (t70) cc_final: 0.8557 (t0) outliers start: 15 outliers final: 6 residues processed: 85 average time/residue: 0.6278 time to fit residues: 55.8664 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN L 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.083048 restraints weight = 9117.296| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.15 r_work: 0.2831 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6484 Z= 0.161 Angle : 0.580 9.838 8826 Z= 0.292 Chirality : 0.043 0.172 1017 Planarity : 0.005 0.052 1102 Dihedral : 4.269 32.785 885 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 13.11 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.42 (0.30), residues: 821 helix: 1.95 (0.30), residues: 336 sheet: 1.17 (0.34), residues: 221 loop : -0.56 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 274 TYR 0.014 0.001 TYR A 422 PHE 0.017 0.001 PHE A 238 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6480) covalent geometry : angle 0.57735 ( 8818) SS BOND : bond 0.00512 ( 4) SS BOND : angle 1.98039 ( 8) hydrogen bonds : bond 0.04172 ( 363) hydrogen bonds : angle 4.55199 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.289 Fit side-chains REVERT: A 34 ASN cc_start: 0.8501 (m-40) cc_final: 0.8269 (m-40) REVERT: A 433 TYR cc_start: 0.8848 (m-80) cc_final: 0.8625 (m-80) REVERT: L 145 ASN cc_start: 0.7747 (t0) cc_final: 0.7284 (t0) REVERT: L 156 GLN cc_start: 0.8018 (mp10) cc_final: 0.7744 (mp10) REVERT: H 89 ASP cc_start: 0.8940 (t70) cc_final: 0.8736 (t0) outliers start: 15 outliers final: 14 residues processed: 87 average time/residue: 0.5664 time to fit residues: 51.6091 Evaluate side-chains 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 155 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN L 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085032 restraints weight = 9094.980| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.14 r_work: 0.2863 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6484 Z= 0.120 Angle : 0.546 9.912 8826 Z= 0.274 Chirality : 0.042 0.185 1017 Planarity : 0.005 0.056 1102 Dihedral : 4.163 32.288 885 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.85 % Allowed : 13.68 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.51 (0.30), residues: 821 helix: 2.06 (0.30), residues: 336 sheet: 1.20 (0.34), residues: 221 loop : -0.57 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 274 TYR 0.011 0.001 TYR A 422 PHE 0.014 0.001 PHE A 238 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.000 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6480) covalent geometry : angle 0.54376 ( 8818) SS BOND : bond 0.00432 ( 4) SS BOND : angle 1.70682 ( 8) hydrogen bonds : bond 0.03572 ( 363) hydrogen bonds : angle 4.42618 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.184 Fit side-chains REVERT: A 17 ARG cc_start: 0.8544 (mpt-90) cc_final: 0.8323 (mmt-90) REVERT: A 34 ASN cc_start: 0.8519 (m-40) cc_final: 0.8305 (m110) REVERT: A 379 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8445 (mmtp) REVERT: A 433 TYR cc_start: 0.8828 (m-80) cc_final: 0.8567 (m-80) REVERT: L 145 ASN cc_start: 0.7736 (t0) cc_final: 0.7269 (t0) REVERT: L 156 GLN cc_start: 0.8027 (mp10) cc_final: 0.7758 (mp10) REVERT: H 89 ASP cc_start: 0.8949 (t70) cc_final: 0.8743 (t0) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.5736 time to fit residues: 51.6251 Evaluate side-chains 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.084307 restraints weight = 9140.041| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.15 r_work: 0.2855 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6484 Z= 0.132 Angle : 0.558 10.035 8826 Z= 0.280 Chirality : 0.042 0.177 1017 Planarity : 0.005 0.062 1102 Dihedral : 4.172 29.940 885 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.85 % Allowed : 13.82 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.49 (0.30), residues: 821 helix: 2.04 (0.30), residues: 336 sheet: 1.20 (0.34), residues: 221 loop : -0.57 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 274 TYR 0.012 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6480) covalent geometry : angle 0.55540 ( 8818) SS BOND : bond 0.00456 ( 4) SS BOND : angle 1.84461 ( 8) hydrogen bonds : bond 0.03768 ( 363) hydrogen bonds : angle 4.43611 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.267 Fit side-chains REVERT: A 34 ASN cc_start: 0.8489 (m-40) cc_final: 0.8287 (m110) REVERT: A 379 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8415 (mmtp) REVERT: A 433 TYR cc_start: 0.8811 (m-80) cc_final: 0.8542 (m-80) REVERT: L 145 ASN cc_start: 0.7729 (t0) cc_final: 0.7269 (t0) REVERT: L 156 GLN cc_start: 0.8033 (mp10) cc_final: 0.7759 (mp10) REVERT: H 89 ASP cc_start: 0.8938 (t70) cc_final: 0.8617 (t0) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.5663 time to fit residues: 50.9321 Evaluate side-chains 89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 0.0270 chunk 61 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.084640 restraints weight = 9000.027| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.14 r_work: 0.2858 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6484 Z= 0.128 Angle : 0.554 10.072 8826 Z= 0.278 Chirality : 0.042 0.178 1017 Planarity : 0.005 0.064 1102 Dihedral : 4.148 28.537 885 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.57 % Allowed : 13.96 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.50 (0.30), residues: 821 helix: 2.06 (0.30), residues: 336 sheet: 1.19 (0.34), residues: 221 loop : -0.56 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 274 TYR 0.012 0.001 TYR A 422 PHE 0.016 0.001 PHE A 238 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6480) covalent geometry : angle 0.55201 ( 8818) SS BOND : bond 0.00445 ( 4) SS BOND : angle 1.80547 ( 8) hydrogen bonds : bond 0.03682 ( 363) hydrogen bonds : angle 4.41446 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.248 Fit side-chains REVERT: A 34 ASN cc_start: 0.8487 (m-40) cc_final: 0.8284 (m110) REVERT: A 433 TYR cc_start: 0.8807 (m-80) cc_final: 0.8540 (m-80) REVERT: L 145 ASN cc_start: 0.7751 (t0) cc_final: 0.7284 (t0) REVERT: L 156 GLN cc_start: 0.8074 (mp10) cc_final: 0.7814 (mp10) REVERT: H 89 ASP cc_start: 0.8937 (t70) cc_final: 0.8620 (t0) outliers start: 11 outliers final: 11 residues processed: 86 average time/residue: 0.5514 time to fit residues: 49.6776 Evaluate side-chains 89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 151 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.084983 restraints weight = 9068.854| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.15 r_work: 0.2865 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6484 Z= 0.124 Angle : 0.551 9.845 8826 Z= 0.276 Chirality : 0.042 0.175 1017 Planarity : 0.005 0.066 1102 Dihedral : 4.133 27.173 885 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.71 % Allowed : 14.25 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.52 (0.30), residues: 821 helix: 2.09 (0.30), residues: 336 sheet: 1.19 (0.34), residues: 221 loop : -0.56 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 274 TYR 0.011 0.001 TYR A 422 PHE 0.015 0.001 PHE A 238 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6480) covalent geometry : angle 0.54869 ( 8818) SS BOND : bond 0.00436 ( 4) SS BOND : angle 1.76295 ( 8) hydrogen bonds : bond 0.03612 ( 363) hydrogen bonds : angle 4.38649 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.34 seconds wall clock time: 36 minutes 4.55 seconds (2164.55 seconds total)