Starting phenix.real_space_refine on Fri Aug 22 17:23:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o54_70123/08_2025/9o54_70123.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o54_70123/08_2025/9o54_70123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o54_70123/08_2025/9o54_70123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o54_70123/08_2025/9o54_70123.map" model { file = "/net/cci-nas-00/data/ceres_data/9o54_70123/08_2025/9o54_70123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o54_70123/08_2025/9o54_70123.cif" } resolution = 3.5 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 29 5.16 5 C 4042 2.51 5 N 1087 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 6433 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3132 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 376} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Chain: "D" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1661 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.27 Number of scatterers: 6433 At special positions: 0 Unit cell: (64.17, 64.17, 138.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 29 16.00 O 1274 8.00 N 1087 7.00 C 4042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " 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: 0.53 Conformation dependent library (CDL) restraints added in 410.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 415 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 405 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 409 " 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 16 sheets defined 17.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.952A pdb=" N ARG A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 243 through 265 removed outlier: 3.598A pdb=" N THR A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.885A pdb=" N GLY A 346 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.714A pdb=" N LYS A 448 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 470 removed outlier: 5.237A pdb=" N SER A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLN A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.728A pdb=" N LYS C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 4.397A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.565A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.023A pdb=" N LYS D 65 " --> pdb=" O THR D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 74 through 77 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 191 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 removed outlier: 3.662A pdb=" N VAL A 66 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 127 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 119 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER A 125 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 99 removed outlier: 3.871A pdb=" N LYS A 95 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N CYS A 225 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N GLN A 281 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU A 227 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG A 283 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 229 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A 285 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 231 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LEU A 334 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS A 226 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N HIS A 336 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 228 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 338 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 230 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 371 removed outlier: 3.765A pdb=" N LYS A 376 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 389 removed outlier: 3.617A pdb=" N ASN A 389 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.506A pdb=" N SER C 25 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 69 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.778A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 13 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AB1, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 139 removed outlier: 5.913A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.645A pdb=" N LEU D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.447A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.447A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.516A pdb=" N SER D 126 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 147 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR D 182 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 156 through 160 removed outlier: 3.875A pdb=" N ASN D 205 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 159 " --> pdb=" O ASN D 203 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.75 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: 2091 1.34 - 1.46: 1555 1.46 - 1.58: 2885 1.58 - 1.70: 1 1.70 - 1.82: 42 Bond restraints: 6574 Sorted by residual: bond pdb=" CG PRO D 153 " pdb=" CD PRO D 153 " ideal model delta sigma weight residual 1.512 1.409 0.103 2.70e-02 1.37e+03 1.44e+01 bond pdb=" CB PRO D 153 " pdb=" CG PRO D 153 " ideal model delta sigma weight residual 1.506 1.598 -0.092 3.90e-02 6.57e+02 5.61e+00 bond pdb=" N PRO D 153 " pdb=" CA PRO D 153 " ideal model delta sigma weight residual 1.468 1.428 0.040 1.70e-02 3.46e+03 5.42e+00 bond pdb=" N PRO D 153 " pdb=" CD PRO D 153 " ideal model delta sigma weight residual 1.474 1.506 -0.032 1.40e-02 5.10e+03 5.32e+00 bond pdb=" CB PRO C 80 " pdb=" CG PRO C 80 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.63e+00 ... (remaining 6569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 8858 3.23 - 6.45: 41 6.45 - 9.68: 8 9.68 - 12.91: 1 12.91 - 16.14: 1 Bond angle restraints: 8909 Sorted by residual: angle pdb=" CA PRO D 153 " pdb=" N PRO D 153 " pdb=" CD PRO D 153 " ideal model delta sigma weight residual 111.50 95.36 16.14 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N PRO D 153 " pdb=" CD PRO D 153 " pdb=" CG PRO D 153 " ideal model delta sigma weight residual 103.80 96.85 6.95 1.20e+00 6.94e-01 3.35e+01 angle pdb=" CA GLU C 165 " pdb=" CB GLU C 165 " pdb=" CG GLU C 165 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 angle pdb=" C PHE D 152 " pdb=" N PRO D 153 " pdb=" CD PRO D 153 " ideal model delta sigma weight residual 120.60 113.13 7.47 2.20e+00 2.07e-01 1.15e+01 angle pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" CD PRO C 80 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.40e+00 5.10e-01 1.15e+01 ... (remaining 8904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3356 17.94 - 35.89: 463 35.89 - 53.83: 103 53.83 - 71.77: 28 71.77 - 89.71: 7 Dihedral angle restraints: 3957 sinusoidal: 1558 harmonic: 2399 Sorted by residual: dihedral pdb=" CA PRO D 153 " pdb=" C PRO D 153 " pdb=" N GLU D 154 " pdb=" CA GLU D 154 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA CYS A 365 " pdb=" CB CYS A 365 " pdb=" SG CYS A 365 " pdb=" SG CYS A 469 " ideal model delta sinusoidal sigma weight residual -73.00 -1.16 -71.84 1 2.00e+01 2.50e-03 1.65e+01 dihedral pdb=" CA TRP A 312 " pdb=" C TRP A 312 " pdb=" N ASP A 313 " pdb=" CA ASP A 313 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 3954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 568 0.028 - 0.056: 261 0.056 - 0.085: 82 0.085 - 0.113: 62 0.113 - 0.141: 9 Chirality restraints: 982 Sorted by residual: chirality pdb=" CA ILE C 29 " pdb=" N ILE C 29 " pdb=" C ILE C 29 " pdb=" CB ILE C 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL A 434 " pdb=" N VAL A 434 " pdb=" C VAL A 434 " pdb=" CB VAL A 434 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE A 149 " pdb=" N ILE A 149 " pdb=" C ILE A 149 " pdb=" CB ILE A 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 979 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 152 " -0.105 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO D 153 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 79 " -0.079 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO C 80 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 172 " 0.060 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO D 173 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " 0.048 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 160 2.68 - 3.24: 6152 3.24 - 3.79: 9832 3.79 - 4.35: 12968 4.35 - 4.90: 21762 Nonbonded interactions: 50874 Sorted by model distance: nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.131 3.040 nonbonded pdb=" ND2 ASN C 34 " pdb=" OE1 GLN C 89 " model vdw 2.164 3.120 nonbonded pdb=" NE2 HIS A 336 " pdb=" OG1 THR A 385 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASN C 137 " pdb=" OG SER C 174 " model vdw 2.265 3.040 nonbonded pdb=" NH2 ARG D 67 " pdb=" OD2 ASP D 90 " model vdw 2.279 3.120 ... (remaining 50869 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 group one per residue 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: 4.020 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.370 Find NCS groups from input model: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 0.103 6583 Z= 0.141 Angle : 0.654 16.136 8921 Z= 0.350 Chirality : 0.042 0.141 982 Planarity : 0.007 0.145 1150 Dihedral : 17.324 89.713 2403 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.28 % Allowed : 28.16 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.25 (0.30), residues: 817 helix: 1.82 (0.56), residues: 74 sheet: -1.23 (0.38), residues: 207 loop : -1.06 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 87 TYR 0.010 0.001 TYR A 304 PHE 0.008 0.001 PHE A 114 TRP 0.010 0.001 TRP A 312 HIS 0.007 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6574) covalent geometry : angle 0.65353 ( 8909) SS BOND : bond 0.00132 ( 6) SS BOND : angle 0.89614 ( 12) hydrogen bonds : bond 0.24251 ( 173) hydrogen bonds : angle 10.50453 ( 474) metal coordination : bond 0.00126 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.257 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.0918 time to fit residues: 11.1444 Evaluate side-chains 87 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 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 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.186453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146436 restraints weight = 8362.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150648 restraints weight = 4143.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153300 restraints weight = 2609.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154607 restraints weight = 1942.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155720 restraints weight = 1651.251| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6583 Z= 0.152 Angle : 0.591 8.578 8921 Z= 0.305 Chirality : 0.043 0.152 982 Planarity : 0.005 0.080 1150 Dihedral : 4.686 42.810 897 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.72 % Allowed : 24.97 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.34 (0.29), residues: 817 helix: 1.23 (0.56), residues: 83 sheet: -1.25 (0.35), residues: 215 loop : -1.09 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 67 TYR 0.010 0.001 TYR C 36 PHE 0.012 0.001 PHE C 98 TRP 0.010 0.001 TRP D 47 HIS 0.005 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6574) covalent geometry : angle 0.58996 ( 8909) SS BOND : bond 0.00167 ( 6) SS BOND : angle 0.99757 ( 12) hydrogen bonds : bond 0.04134 ( 173) hydrogen bonds : angle 6.93800 ( 474) metal coordination : bond 0.00251 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 119 VAL cc_start: 0.8838 (t) cc_final: 0.8469 (m) REVERT: A 278 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: A 341 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: C 108 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6867 (mtm110) REVERT: D 82 GLN cc_start: 0.7312 (tp40) cc_final: 0.6911 (tm-30) outliers start: 34 outliers final: 20 residues processed: 115 average time/residue: 0.0728 time to fit residues: 11.1858 Evaluate side-chains 109 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.0010 chunk 75 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146121 restraints weight = 8276.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150495 restraints weight = 4037.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153174 restraints weight = 2526.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154766 restraints weight = 1884.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155750 restraints weight = 1582.367| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6583 Z= 0.116 Angle : 0.549 8.038 8921 Z= 0.281 Chirality : 0.042 0.148 982 Planarity : 0.005 0.065 1150 Dihedral : 4.510 47.374 897 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.16 % Allowed : 24.55 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.36 (0.29), residues: 817 helix: 1.34 (0.55), residues: 82 sheet: -1.26 (0.37), residues: 205 loop : -1.14 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.010 0.001 TYR A 304 PHE 0.011 0.001 PHE D 152 TRP 0.009 0.001 TRP D 47 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6574) covalent geometry : angle 0.54815 ( 8909) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.86001 ( 12) hydrogen bonds : bond 0.03407 ( 173) hydrogen bonds : angle 6.19354 ( 474) metal coordination : bond 0.00180 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7554 (m-30) cc_final: 0.6908 (m-30) REVERT: A 119 VAL cc_start: 0.8824 (t) cc_final: 0.8473 (m) REVERT: A 132 ARG cc_start: 0.6255 (tpm170) cc_final: 0.5968 (tpm170) REVERT: A 149 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 341 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: C 18 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7341 (ttt-90) REVERT: C 90 GLN cc_start: 0.8365 (pp30) cc_final: 0.7937 (pp30) REVERT: C 108 ARG cc_start: 0.7130 (mtm-85) cc_final: 0.6874 (mtm110) outliers start: 30 outliers final: 21 residues processed: 114 average time/residue: 0.0776 time to fit residues: 11.6004 Evaluate side-chains 111 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 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 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.187101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146806 restraints weight = 8547.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151061 restraints weight = 4145.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153656 restraints weight = 2582.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155180 restraints weight = 1924.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.155946 restraints weight = 1623.300| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6583 Z= 0.146 Angle : 0.567 9.077 8921 Z= 0.288 Chirality : 0.043 0.147 982 Planarity : 0.005 0.058 1150 Dihedral : 4.587 50.567 897 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.41 % Allowed : 23.99 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.41 (0.29), residues: 817 helix: 1.26 (0.55), residues: 83 sheet: -1.25 (0.36), residues: 204 loop : -1.18 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.011 0.001 TYR D 182 PHE 0.012 0.001 PHE C 98 TRP 0.011 0.001 TRP D 47 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6574) covalent geometry : angle 0.56612 ( 8909) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.88197 ( 12) hydrogen bonds : bond 0.03377 ( 173) hydrogen bonds : angle 5.97559 ( 474) metal coordination : bond 0.00262 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7617 (m-30) cc_final: 0.6937 (m-30) REVERT: A 119 VAL cc_start: 0.8885 (t) cc_final: 0.8554 (m) REVERT: A 132 ARG cc_start: 0.6243 (tpm170) cc_final: 0.5950 (tpm170) REVERT: A 149 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8205 (mm) REVERT: A 278 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: A 341 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: C 90 GLN cc_start: 0.8420 (pp30) cc_final: 0.7974 (pp30) REVERT: C 108 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6770 (mtm110) outliers start: 39 outliers final: 26 residues processed: 119 average time/residue: 0.0756 time to fit residues: 12.0158 Evaluate side-chains 117 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 0.0010 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.190651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149652 restraints weight = 8580.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153988 restraints weight = 4181.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156655 restraints weight = 2609.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.158230 restraints weight = 1942.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158979 restraints weight = 1634.445| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6583 Z= 0.103 Angle : 0.543 9.272 8921 Z= 0.274 Chirality : 0.042 0.149 982 Planarity : 0.004 0.051 1150 Dihedral : 4.431 54.478 897 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.85 % Allowed : 25.38 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.26 (0.29), residues: 817 helix: 1.36 (0.55), residues: 83 sheet: -1.11 (0.36), residues: 206 loop : -1.10 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 53 TYR 0.011 0.001 TYR A 304 PHE 0.014 0.001 PHE A 323 TRP 0.009 0.001 TRP D 47 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6574) covalent geometry : angle 0.54249 ( 8909) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.75750 ( 12) hydrogen bonds : bond 0.02997 ( 173) hydrogen bonds : angle 5.62769 ( 474) metal coordination : bond 0.00145 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7558 (m-30) cc_final: 0.6906 (m-30) REVERT: A 119 VAL cc_start: 0.8833 (t) cc_final: 0.8522 (m) REVERT: A 132 ARG cc_start: 0.6237 (tpm170) cc_final: 0.6018 (tpm170) REVERT: A 149 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 278 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: A 341 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7898 (pt0) REVERT: C 18 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7353 (ttt-90) REVERT: C 90 GLN cc_start: 0.8322 (pp30) cc_final: 0.7872 (pp30) REVERT: C 108 ARG cc_start: 0.7082 (mtm-85) cc_final: 0.6714 (mtt180) outliers start: 35 outliers final: 22 residues processed: 127 average time/residue: 0.0875 time to fit residues: 14.5075 Evaluate side-chains 117 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151167 restraints weight = 8596.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155539 restraints weight = 4189.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.158263 restraints weight = 2615.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159717 restraints weight = 1942.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.160775 restraints weight = 1646.602| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6583 Z= 0.094 Angle : 0.534 8.334 8921 Z= 0.269 Chirality : 0.042 0.154 982 Planarity : 0.004 0.049 1150 Dihedral : 4.351 57.135 897 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.44 % Allowed : 26.49 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.11 (0.29), residues: 817 helix: 1.46 (0.56), residues: 82 sheet: -0.95 (0.37), residues: 206 loop : -1.02 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.012 0.001 TYR A 304 PHE 0.009 0.001 PHE A 323 TRP 0.008 0.001 TRP D 47 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6574) covalent geometry : angle 0.53376 ( 8909) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.70167 ( 12) hydrogen bonds : bond 0.02869 ( 173) hydrogen bonds : angle 5.43669 ( 474) metal coordination : bond 0.00119 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7477 (m-30) cc_final: 0.6872 (m-30) REVERT: A 119 VAL cc_start: 0.8803 (t) cc_final: 0.8492 (m) REVERT: A 132 ARG cc_start: 0.6231 (tpm170) cc_final: 0.6014 (tpm170) REVERT: A 149 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 278 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: A 341 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: C 36 TYR cc_start: 0.8585 (m-80) cc_final: 0.8295 (m-80) REVERT: C 90 GLN cc_start: 0.8355 (pp30) cc_final: 0.7842 (pp30) outliers start: 32 outliers final: 23 residues processed: 117 average time/residue: 0.0682 time to fit residues: 10.6793 Evaluate side-chains 113 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 20 optimal weight: 0.0470 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.190327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150495 restraints weight = 8458.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154855 restraints weight = 4099.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157502 restraints weight = 2534.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158957 restraints weight = 1883.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159961 restraints weight = 1588.192| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6583 Z= 0.102 Angle : 0.554 9.360 8921 Z= 0.276 Chirality : 0.042 0.151 982 Planarity : 0.004 0.049 1150 Dihedral : 4.371 58.831 897 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.16 % Allowed : 27.18 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.08 (0.29), residues: 817 helix: 1.48 (0.55), residues: 82 sheet: -0.87 (0.36), residues: 213 loop : -1.02 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.009 0.001 TYR D 151 PHE 0.010 0.001 PHE A 114 TRP 0.011 0.001 TRP C 35 HIS 0.003 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6574) covalent geometry : angle 0.55350 ( 8909) SS BOND : bond 0.00098 ( 6) SS BOND : angle 0.64660 ( 12) hydrogen bonds : bond 0.02875 ( 173) hydrogen bonds : angle 5.35356 ( 474) metal coordination : bond 0.00142 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 VAL cc_start: 0.8823 (t) cc_final: 0.8529 (m) REVERT: A 149 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8118 (mm) REVERT: A 278 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: A 341 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: A 456 GLN cc_start: 0.7829 (tp40) cc_final: 0.7592 (tp40) REVERT: C 90 GLN cc_start: 0.8208 (pp30) cc_final: 0.7713 (pp30) REVERT: C 108 ARG cc_start: 0.7408 (mtm110) cc_final: 0.7132 (mtt90) outliers start: 30 outliers final: 24 residues processed: 117 average time/residue: 0.0742 time to fit residues: 11.5439 Evaluate side-chains 112 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.184936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144118 restraints weight = 8581.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148324 restraints weight = 4234.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150952 restraints weight = 2670.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152274 restraints weight = 1998.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153332 restraints weight = 1706.353| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6583 Z= 0.201 Angle : 0.633 9.100 8921 Z= 0.321 Chirality : 0.045 0.182 982 Planarity : 0.005 0.048 1150 Dihedral : 4.869 58.710 897 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.85 % Allowed : 26.77 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.23 (0.29), residues: 817 helix: 1.78 (0.56), residues: 77 sheet: -1.12 (0.37), residues: 211 loop : -1.10 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.019 0.002 TYR A 304 PHE 0.023 0.002 PHE C 98 TRP 0.024 0.002 TRP A 111 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 6574) covalent geometry : angle 0.63259 ( 8909) SS BOND : bond 0.00184 ( 6) SS BOND : angle 0.97965 ( 12) hydrogen bonds : bond 0.03572 ( 173) hydrogen bonds : angle 5.73975 ( 474) metal coordination : bond 0.00417 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6454 (mt0) REVERT: A 119 VAL cc_start: 0.8997 (t) cc_final: 0.8718 (m) REVERT: A 278 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: A 341 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: C 90 GLN cc_start: 0.8345 (pp30) cc_final: 0.7770 (pp30) outliers start: 35 outliers final: 26 residues processed: 119 average time/residue: 0.0664 time to fit residues: 10.6739 Evaluate side-chains 120 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 30 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.190493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149932 restraints weight = 8621.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154279 restraints weight = 4188.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156980 restraints weight = 2610.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158344 restraints weight = 1942.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159455 restraints weight = 1651.523| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6583 Z= 0.103 Angle : 0.585 10.338 8921 Z= 0.292 Chirality : 0.043 0.154 982 Planarity : 0.004 0.055 1150 Dihedral : 4.572 57.130 897 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.16 % Allowed : 27.18 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.12 (0.29), residues: 817 helix: 1.44 (0.55), residues: 82 sheet: -0.94 (0.37), residues: 206 loop : -1.02 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.013 0.001 TYR A 304 PHE 0.009 0.001 PHE A 323 TRP 0.022 0.002 TRP D 160 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6574) covalent geometry : angle 0.58457 ( 8909) SS BOND : bond 0.00179 ( 6) SS BOND : angle 0.72718 ( 12) hydrogen bonds : bond 0.02972 ( 173) hydrogen bonds : angle 5.40754 ( 474) metal coordination : bond 0.00117 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6419 (mt0) REVERT: A 119 VAL cc_start: 0.8884 (t) cc_final: 0.8598 (m) REVERT: A 139 ARG cc_start: 0.7567 (ttt90) cc_final: 0.7074 (ttt90) REVERT: A 149 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 278 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: A 341 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: C 90 GLN cc_start: 0.8120 (pp30) cc_final: 0.7585 (pp30) outliers start: 30 outliers final: 23 residues processed: 113 average time/residue: 0.0731 time to fit residues: 11.0922 Evaluate side-chains 112 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 77 optimal weight: 0.0050 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.189728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149666 restraints weight = 8474.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153871 restraints weight = 4153.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156515 restraints weight = 2610.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157835 restraints weight = 1956.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.158912 restraints weight = 1668.778| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6583 Z= 0.118 Angle : 0.584 10.437 8921 Z= 0.290 Chirality : 0.043 0.150 982 Planarity : 0.004 0.051 1150 Dihedral : 4.560 56.718 897 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.74 % Allowed : 27.60 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.09 (0.29), residues: 817 helix: 1.36 (0.55), residues: 83 sheet: -0.91 (0.37), residues: 206 loop : -0.99 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.008 0.001 TYR D 151 PHE 0.013 0.001 PHE A 114 TRP 0.020 0.002 TRP D 160 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6574) covalent geometry : angle 0.58415 ( 8909) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.73750 ( 12) hydrogen bonds : bond 0.03008 ( 173) hydrogen bonds : angle 5.37943 ( 474) metal coordination : bond 0.00190 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6447 (mt0) REVERT: A 119 VAL cc_start: 0.8890 (t) cc_final: 0.8609 (m) REVERT: A 139 ARG cc_start: 0.7565 (ttt90) cc_final: 0.7062 (ttt90) REVERT: A 149 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8113 (mm) REVERT: A 278 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: A 341 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: C 90 GLN cc_start: 0.8171 (pp30) cc_final: 0.7606 (pp30) outliers start: 27 outliers final: 23 residues processed: 105 average time/residue: 0.0615 time to fit residues: 8.8088 Evaluate side-chains 109 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 37 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 39 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: A 112 GLN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.189159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149189 restraints weight = 8528.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153384 restraints weight = 4158.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156043 restraints weight = 2607.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157430 restraints weight = 1947.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158323 restraints weight = 1655.209| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6583 Z= 0.132 Angle : 0.590 10.287 8921 Z= 0.293 Chirality : 0.043 0.150 982 Planarity : 0.004 0.050 1150 Dihedral : 4.566 56.590 897 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.88 % Allowed : 27.32 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.11 (0.29), residues: 817 helix: 1.34 (0.55), residues: 83 sheet: -0.90 (0.38), residues: 198 loop : -1.02 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.015 0.001 TYR A 304 PHE 0.011 0.001 PHE C 98 TRP 0.018 0.002 TRP D 160 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6574) covalent geometry : angle 0.58944 ( 8909) SS BOND : bond 0.00129 ( 6) SS BOND : angle 0.77350 ( 12) hydrogen bonds : bond 0.03089 ( 173) hydrogen bonds : angle 5.40584 ( 474) metal coordination : bond 0.00239 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1171.16 seconds wall clock time: 20 minutes 54.32 seconds (1254.32 seconds total)