Starting phenix.real_space_refine on Sat May 10 13:16:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wre_37775/05_2025/8wre_37775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wre_37775/05_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_37775/05_2025/8wre_37775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wre_37775/05_2025/8wre_37775.map" model { file = "/net/cci-nas-00/data/ceres_data/8wre_37775/05_2025/8wre_37775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wre_37775/05_2025/8wre_37775.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.18, per 1000 atoms: 0.66 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: 1.39 Conformation dependent library (CDL) restraints added in 846.3 milliseconds 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: 0.89 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: 2.25 Time building geometry restraints manager: 1.66 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.840 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (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 TRP 0.009 0.001 TRP H 114 HIS 0.002 0.000 HIS H 175 PHE 0.019 0.001 PHE A 166 TYR 0.013 0.001 TYR A 433 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.13501 ( 363) hydrogen bonds : angle 6.23849 ( 1080) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.90320 ( 8) covalent geometry : bond 0.00307 ( 6480) covalent geometry : angle 0.54249 ( 8818) *********************** 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 : 0.694 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: 1.2499 time to fit residues: 119.3836 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 : 0.658 ------------------------------------------------------------------------------- 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 69 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3317 r_free = 0.3317 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.083342 restraints weight = 8968.498| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.12 r_work: 0.2831 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6484 Z= 0.172 Angle : 0.592 10.044 8826 Z= 0.303 Chirality : 0.044 0.169 1017 Planarity : 0.005 0.044 1102 Dihedral : 4.569 47.715 887 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 6.13 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.30), residues: 821 helix: 1.76 (0.29), residues: 333 sheet: 1.52 (0.35), residues: 213 loop : -0.64 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.018 0.002 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.003 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 363) hydrogen bonds : angle 4.94087 ( 1080) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.89234 ( 8) covalent geometry : bond 0.00429 ( 6480) covalent geometry : angle 0.59173 ( 8818) *********************** 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 95 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.676 Fit side-chains REVERT: A 433 TYR cc_start: 0.8844 (m-80) cc_final: 0.8578 (m-80) REVERT: L 211 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7807 (ttm170) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 1.3900 time to fit residues: 126.4698 Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain L residue 157 ASN Chi-restraints excluded: chain L residue 211 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 65 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3333 r_free = 0.3333 target = 0.110306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.084524 restraints weight = 9022.184| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.13 r_work: 0.2853 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1053 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= 0.131 Angle : 0.553 10.164 8826 Z= 0.280 Chirality : 0.042 0.174 1017 Planarity : 0.005 0.044 1102 Dihedral : 4.392 45.008 887 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.57 % Allowed : 9.69 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 821 helix: 1.89 (0.30), residues: 335 sheet: 1.46 (0.35), residues: 216 loop : -0.58 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.015 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.011 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 363) hydrogen bonds : angle 4.67515 ( 1080) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.70430 ( 8) covalent geometry : bond 0.00313 ( 6480) covalent geometry : angle 0.55239 ( 8818) *********************** 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: 11 poor density : 77 time to evaluate : 0.788 Fit side-chains REVERT: A 433 TYR cc_start: 0.8815 (m-80) cc_final: 0.8555 (m-80) REVERT: H 89 ASP cc_start: 0.8880 (t70) cc_final: 0.8644 (t0) outliers start: 11 outliers final: 2 residues processed: 80 average time/residue: 1.3843 time to fit residues: 116.4880 Evaluate side-chains 72 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.110955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.085342 restraints weight = 9099.397| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.12 r_work: 0.2867 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1163 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= 0.120 Angle : 0.540 9.339 8826 Z= 0.272 Chirality : 0.042 0.178 1017 Planarity : 0.004 0.044 1102 Dihedral : 4.262 42.730 885 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.85 % Allowed : 11.68 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.30), residues: 821 helix: 2.00 (0.30), residues: 335 sheet: 1.49 (0.35), residues: 214 loop : -0.60 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.015 0.001 PHE A 238 TYR 0.011 0.001 TYR A 422 ARG 0.008 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 363) hydrogen bonds : angle 4.56224 ( 1080) SS BOND : bond 0.00776 ( 4) SS BOND : angle 1.03707 ( 8) covalent geometry : bond 0.00282 ( 6480) covalent geometry : angle 0.53909 ( 8818) *********************** 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 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.746 Fit side-chains REVERT: A 278 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: A 433 TYR cc_start: 0.8813 (m-80) cc_final: 0.8570 (m-80) REVERT: H 89 ASP cc_start: 0.8892 (t70) cc_final: 0.8635 (t0) REVERT: H 193 THR cc_start: 0.9085 (m) cc_final: 0.8883 (p) outliers start: 13 outliers final: 6 residues processed: 77 average time/residue: 1.4118 time to fit residues: 113.7389 Evaluate side-chains 77 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 157 ASN Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain H residue 5 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.106838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.080841 restraints weight = 9117.976| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.14 r_work: 0.2793 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6484 Z= 0.217 Angle : 0.626 9.899 8826 Z= 0.318 Chirality : 0.045 0.163 1017 Planarity : 0.005 0.046 1102 Dihedral : 4.492 35.751 885 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.28 % Allowed : 12.11 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.30), residues: 821 helix: 1.69 (0.29), residues: 336 sheet: 1.20 (0.35), residues: 220 loop : -0.54 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS H 175 PHE 0.019 0.002 PHE A 238 TYR 0.017 0.002 TYR A 422 ARG 0.010 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 363) hydrogen bonds : angle 4.78678 ( 1080) SS BOND : bond 0.00572 ( 4) SS BOND : angle 2.33017 ( 8) covalent geometry : bond 0.00547 ( 6480) covalent geometry : angle 0.62203 ( 8818) *********************** 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: 16 poor density : 77 time to evaluate : 0.702 Fit side-chains REVERT: A 433 TYR cc_start: 0.8889 (m-80) cc_final: 0.8653 (m-80) REVERT: L 211 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7722 (ttm170) REVERT: H 89 ASP cc_start: 0.8950 (t70) cc_final: 0.8692 (t0) REVERT: H 193 THR cc_start: 0.9184 (m) cc_final: 0.8963 (p) outliers start: 16 outliers final: 7 residues processed: 82 average time/residue: 1.3560 time to fit residues: 116.4579 Evaluate side-chains 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 195 GLU Chi-restraints excluded: chain L residue 211 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL 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 17 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.107218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.081262 restraints weight = 9078.538| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.13 r_work: 0.2799 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1447 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= 0.198 Angle : 0.611 9.831 8826 Z= 0.311 Chirality : 0.044 0.169 1017 Planarity : 0.005 0.055 1102 Dihedral : 4.499 33.516 885 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.85 % Allowed : 12.25 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 821 helix: 1.67 (0.29), residues: 336 sheet: 1.09 (0.34), residues: 221 loop : -0.62 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS H 175 PHE 0.018 0.002 PHE A 238 TYR 0.016 0.002 TYR A 422 ARG 0.011 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 363) hydrogen bonds : angle 4.75865 ( 1080) SS BOND : bond 0.00563 ( 4) SS BOND : angle 2.37162 ( 8) covalent geometry : bond 0.00497 ( 6480) covalent geometry : angle 0.60681 ( 8818) *********************** 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 101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.697 Fit side-chains REVERT: A 206 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8056 (ttm) REVERT: A 433 TYR cc_start: 0.8906 (m-80) cc_final: 0.8671 (m-80) REVERT: L 145 ASN cc_start: 0.7820 (t0) cc_final: 0.7401 (t0) REVERT: L 156 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7866 (OUTLIER) REVERT: H 89 ASP cc_start: 0.9000 (t70) cc_final: 0.8752 (t0) REVERT: H 193 THR cc_start: 0.9187 (m) cc_final: 0.8981 (p) outliers start: 20 outliers final: 14 residues processed: 90 average time/residue: 1.2505 time to fit residues: 118.2215 Evaluate side-chains 94 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 283 THR 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 A residue 435 ILE Chi-restraints excluded: chain L residue 156 GLN 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 65 LYS Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 151 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 190 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 = 0.3311 r_free = 0.3311 target = 0.108700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.083089 restraints weight = 8993.945| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.07 r_work: 0.2834 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6484 Z= 0.145 Angle : 0.572 9.653 8826 Z= 0.290 Chirality : 0.043 0.179 1017 Planarity : 0.005 0.055 1102 Dihedral : 4.364 32.492 885 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.85 % Allowed : 13.39 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.30), residues: 821 helix: 1.83 (0.30), residues: 336 sheet: 1.20 (0.35), residues: 219 loop : -0.65 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.016 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.012 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 363) hydrogen bonds : angle 4.60696 ( 1080) SS BOND : bond 0.00410 ( 4) SS BOND : angle 1.72585 ( 8) covalent geometry : bond 0.00353 ( 6480) covalent geometry : angle 0.56940 ( 8818) *********************** 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 100 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.706 Fit side-chains REVERT: A 206 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: A 278 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: A 433 TYR cc_start: 0.8832 (m-80) cc_final: 0.8554 (m-80) REVERT: L 145 ASN cc_start: 0.7759 (t0) cc_final: 0.7334 (t0) REVERT: L 156 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: L 211 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7702 (ttm170) REVERT: H 89 ASP cc_start: 0.8972 (t70) cc_final: 0.8718 (t0) outliers start: 20 outliers final: 10 residues processed: 88 average time/residue: 1.2929 time to fit residues: 119.2129 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 : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 320 MET 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 156 GLN Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 211 ARG Chi-restraints excluded: chain H residue 5 GLN 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 74 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.108925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.083041 restraints weight = 9012.634| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.13 r_work: 0.2832 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6484 Z= 0.148 Angle : 0.572 9.513 8826 Z= 0.289 Chirality : 0.043 0.174 1017 Planarity : 0.005 0.056 1102 Dihedral : 4.332 30.410 885 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.42 % Allowed : 13.82 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.30), residues: 821 helix: 1.86 (0.30), residues: 336 sheet: 1.13 (0.35), residues: 221 loop : -0.62 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.017 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.013 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 363) hydrogen bonds : angle 4.57648 ( 1080) SS BOND : bond 0.00471 ( 4) SS BOND : angle 1.73248 ( 8) covalent geometry : bond 0.00363 ( 6480) covalent geometry : angle 0.56951 ( 8818) *********************** 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 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.696 Fit side-chains REVERT: A 206 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8021 (ttm) REVERT: A 433 TYR cc_start: 0.8820 (m-80) cc_final: 0.8543 (m-80) REVERT: L 145 ASN cc_start: 0.7759 (t0) cc_final: 0.7332 (t0) REVERT: H 89 ASP cc_start: 0.8972 (t70) cc_final: 0.8727 (t0) outliers start: 17 outliers final: 11 residues processed: 85 average time/residue: 1.1866 time to fit residues: 106.2131 Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 283 THR 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 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 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.0670 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.110437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.084670 restraints weight = 9092.427| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.15 r_work: 0.2858 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1437 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= 0.122 Angle : 0.548 9.662 8826 Z= 0.276 Chirality : 0.042 0.183 1017 Planarity : 0.005 0.059 1102 Dihedral : 4.193 29.187 885 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.99 % Allowed : 14.10 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.30), residues: 821 helix: 2.00 (0.30), residues: 336 sheet: 1.26 (0.35), residues: 219 loop : -0.65 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.000 HIS H 175 PHE 0.014 0.001 PHE A 238 TYR 0.010 0.001 TYR A 422 ARG 0.014 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 363) hydrogen bonds : angle 4.42998 ( 1080) SS BOND : bond 0.00404 ( 4) SS BOND : angle 1.69051 ( 8) covalent geometry : bond 0.00291 ( 6480) covalent geometry : angle 0.54590 ( 8818) *********************** 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 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.642 Fit side-chains REVERT: A 17 ARG cc_start: 0.8555 (mpt-90) cc_final: 0.8321 (mmt-90) REVERT: A 206 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8016 (ttm) REVERT: A 433 TYR cc_start: 0.8773 (m-80) cc_final: 0.8522 (m-80) REVERT: L 145 ASN cc_start: 0.7723 (t0) cc_final: 0.7292 (t0) REVERT: H 89 ASP cc_start: 0.8934 (t70) cc_final: 0.8689 (t0) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 1.2030 time to fit residues: 111.2409 Evaluate side-chains 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 283 THR 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 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 65 LYS 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 4 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.110079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.084261 restraints weight = 9039.484| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.13 r_work: 0.2848 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1481 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= 0.130 Angle : 0.557 9.908 8826 Z= 0.280 Chirality : 0.042 0.177 1017 Planarity : 0.005 0.064 1102 Dihedral : 4.191 27.489 885 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.71 % Allowed : 14.53 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.30), residues: 821 helix: 2.00 (0.30), residues: 336 sheet: 1.17 (0.35), residues: 221 loop : -0.59 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.016 0.001 PHE A 238 TYR 0.011 0.001 TYR A 422 ARG 0.015 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 363) hydrogen bonds : angle 4.43922 ( 1080) SS BOND : bond 0.00459 ( 4) SS BOND : angle 1.81033 ( 8) covalent geometry : bond 0.00316 ( 6480) covalent geometry : angle 0.55488 ( 8818) ********************** 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 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.703 Fit side-chains REVERT: A 206 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8061 (ttm) REVERT: A 433 TYR cc_start: 0.8816 (m-80) cc_final: 0.8555 (m-80) REVERT: L 145 ASN cc_start: 0.7749 (t0) cc_final: 0.7327 (t0) REVERT: H 89 ASP cc_start: 0.8952 (t70) cc_final: 0.8734 (t0) outliers start: 12 outliers final: 11 residues processed: 85 average time/residue: 1.2281 time to fit residues: 109.7016 Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 283 THR 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 195 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 65 LYS 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 23 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.111255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085424 restraints weight = 9134.369| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.14 r_work: 0.2867 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6484 Z= 0.116 Angle : 0.546 9.975 8826 Z= 0.273 Chirality : 0.042 0.180 1017 Planarity : 0.005 0.062 1102 Dihedral : 4.107 26.182 885 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.85 % Allowed : 14.53 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 821 helix: 2.09 (0.30), residues: 335 sheet: 1.21 (0.35), residues: 221 loop : -0.58 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 175 PHE 0.015 0.001 PHE A 238 TYR 0.010 0.001 TYR A 422 ARG 0.014 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 363) hydrogen bonds : angle 4.35095 ( 1080) SS BOND : bond 0.00438 ( 4) SS BOND : angle 1.71222 ( 8) covalent geometry : bond 0.00275 ( 6480) covalent geometry : angle 0.54407 ( 8818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4292.44 seconds wall clock time: 74 minutes 50.66 seconds (4490.66 seconds total)