Starting phenix.real_space_refine on Fri Oct 23 00:50:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7i_61204/10_2026/9j7i_61204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7i_61204/10_2026/9j7i_61204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j7i_61204/10_2026/9j7i_61204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7i_61204/10_2026/9j7i_61204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j7i_61204/10_2026/9j7i_61204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7i_61204/10_2026/9j7i_61204.map" } resolution = 3.55 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4680 2.51 5 N 1228 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7284 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3621 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Modifications used: {'COO': 2} Link IDs: {'TRANS': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GGL%COO:plan-2': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: C, D Time building chain proxies: 2.72, per 1000 atoms: 0.37 Number of scatterers: 7284 At special positions: 0 Unit cell: (89.445, 83.415, 80.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1354 8.00 N 1228 7.00 C 4680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 322.4 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 40.8% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.517A pdb=" N LEU A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.671A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 189 through 204 removed outlier: 4.245A pdb=" N GLN A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 removed outlier: 4.063A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix removed outlier: 3.505A pdb=" N GLU A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.598A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'C' and resid 66 through 83 removed outlier: 3.517A pdb=" N LEU C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 146 through 160 removed outlier: 3.671A pdb=" N PHE C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 189 through 204 removed outlier: 4.245A pdb=" N GLN C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 233 removed outlier: 4.063A pdb=" N GLU C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 272 through 287 Proline residue: C 278 - end of helix removed outlier: 3.505A pdb=" N GLU C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 329 through 336 removed outlier: 3.598A pdb=" N PHE C 333 " --> pdb=" O GLY C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'C' and resid 451 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 529 through 533 Processing sheet with id=1, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.631A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 37 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 236 through 237 removed outlier: 9.000A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 236 through 237 removed outlier: 4.364A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 318 through 322 Processing sheet with id=5, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=6, first strand: chain 'A' and resid 509 through 511 Processing sheet with id=7, first strand: chain 'C' and resid 26 through 28 removed outlier: 5.631A pdb=" N ILE C 32 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG C 96 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 34 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE C 98 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY C 36 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 33 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA C 140 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 37 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL C 165 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 141 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN C 164 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 236 through 237 removed outlier: 9.000A pdb=" N GLU C 241 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR C 211 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE C 243 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA C 213 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 236 through 237 removed outlier: 4.364A pdb=" N VAL C 266 " --> pdb=" O TRP C 208 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 318 through 322 Processing sheet with id=11, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=12, first strand: chain 'C' and resid 509 through 511 284 hydrogen bonds defined for protein. 786 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: 1.22 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1480 1.33 - 1.45: 1828 1.45 - 1.57: 4116 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 7454 Sorted by residual: bond pdb=" N ILE C 162 " pdb=" CA ILE C 162 " ideal model delta sigma weight residual 1.460 1.493 -0.032 7.30e-03 1.88e+04 1.95e+01 bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.460 1.493 -0.032 7.30e-03 1.88e+04 1.95e+01 bond pdb=" N GLY C 210 " pdb=" CA GLY C 210 " ideal model delta sigma weight residual 1.442 1.475 -0.034 7.70e-03 1.69e+04 1.91e+01 bond pdb=" N GLY A 210 " pdb=" CA GLY A 210 " ideal model delta sigma weight residual 1.442 1.475 -0.034 7.70e-03 1.69e+04 1.91e+01 bond pdb=" N VAL C 508 " pdb=" CA VAL C 508 " ideal model delta sigma weight residual 1.456 1.492 -0.035 9.50e-03 1.11e+04 1.39e+01 ... (remaining 7449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7354 1.57 - 3.14: 2418 3.14 - 4.71: 314 4.71 - 6.27: 10 6.27 - 7.84: 4 Bond angle restraints: 10100 Sorted by residual: angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 113.53 109.02 4.51 9.80e-01 1.04e+00 2.12e+01 angle pdb=" N VAL C 508 " pdb=" CA VAL C 508 " pdb=" C VAL C 508 " ideal model delta sigma weight residual 113.53 109.02 4.51 9.80e-01 1.04e+00 2.12e+01 angle pdb=" N ILE A 409 " pdb=" CA ILE A 409 " pdb=" C ILE A 409 " ideal model delta sigma weight residual 113.43 108.46 4.97 1.09e+00 8.42e-01 2.08e+01 angle pdb=" N ILE C 409 " pdb=" CA ILE C 409 " pdb=" C ILE C 409 " ideal model delta sigma weight residual 113.43 108.46 4.97 1.09e+00 8.42e-01 2.08e+01 angle pdb=" N ILE C 259 " pdb=" CA ILE C 259 " pdb=" C ILE C 259 " ideal model delta sigma weight residual 110.42 106.36 4.06 9.60e-01 1.09e+00 1.79e+01 ... (remaining 10095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 3912 15.26 - 30.52: 302 30.52 - 45.77: 82 45.77 - 61.03: 62 61.03 - 76.29: 16 Dihedral angle restraints: 4374 sinusoidal: 1724 harmonic: 2650 Sorted by residual: dihedral pdb=" CA VAL D 2 " pdb=" C VAL D 2 " pdb=" N GLY D 3 " pdb=" CA GLY D 3 " ideal model delta harmonic sigma weight residual -180.00 -103.71 -76.29 0 5.00e+00 4.00e-02 2.33e+02 dihedral pdb=" CA VAL B 2 " pdb=" C VAL B 2 " pdb=" N GLY B 3 " pdb=" CA GLY B 3 " ideal model delta harmonic sigma weight residual -180.00 -103.71 -76.29 0 5.00e+00 4.00e-02 2.33e+02 dihedral pdb=" CA ASN C 541 " pdb=" CB ASN C 541 " pdb=" CG ASN C 541 " pdb=" OD1 ASN C 541 " ideal model delta sinusoidal sigma weight residual 120.00 177.08 -57.08 2 2.00e+01 2.50e-03 8.46e+00 ... (remaining 4371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 274 0.047 - 0.094: 302 0.094 - 0.141: 336 0.141 - 0.187: 158 0.187 - 0.234: 38 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CA ARG C 520 " pdb=" N ARG C 520 " pdb=" C ARG C 520 " pdb=" CB ARG C 520 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ARG A 520 " pdb=" N ARG A 520 " pdb=" C ARG A 520 " pdb=" CB ARG A 520 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE C 259 " pdb=" N ILE C 259 " pdb=" C ILE C 259 " pdb=" CB ILE C 259 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1105 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 96 " -0.282 9.50e-02 1.11e+02 1.27e-01 9.84e+00 pdb=" NE ARG C 96 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 96 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 96 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 96 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 96 " 0.282 9.50e-02 1.11e+02 1.27e-01 9.84e+00 pdb=" NE ARG A 96 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 96 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 96 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 96 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 441 " -0.266 9.50e-02 1.11e+02 1.19e-01 8.73e+00 pdb=" NE ARG A 441 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 441 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 441 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 441 " -0.009 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1886 2.82 - 3.34: 8220 3.34 - 3.86: 12739 3.86 - 4.38: 15488 4.38 - 4.90: 24099 Nonbonded interactions: 62432 Sorted by model distance: nonbonded pdb=" O GLU A 405 " pdb=" CG2 THR A 406 " model vdw 2.298 3.460 nonbonded pdb=" O GLU C 405 " pdb=" CG2 THR C 406 " model vdw 2.298 3.460 nonbonded pdb=" CG PRO A 55 " pdb=" CE2 TYR C 161 " model vdw 2.298 3.740 nonbonded pdb=" CE2 TYR A 161 " pdb=" CG PRO C 55 " model vdw 2.298 3.740 nonbonded pdb=" OE2 GLU A 350 " pdb=" OE2 GLU A 354 " model vdw 2.318 3.040 ... (remaining 62427 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 0.012 0.088 7456 Z= 0.961 Angle : 1.435 7.842 10100 Z= 1.123 Chirality : 0.103 0.234 1108 Planarity : 0.011 0.127 1296 Dihedral : 15.225 76.290 2666 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 37.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.31 % Allowed : 9.51 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 are not related in a simple way. whole: -2.86 (0.25), residues: 896 helix: -1.21 (0.27), residues: 316 sheet: -2.45 (0.40), residues: 136 loop : -2.20 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 96 TYR 0.007 0.001 TYR A 514 PHE 0.012 0.002 PHE A 76 TRP 0.012 0.001 TRP A 352 HIS 0.002 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.01233 / 0.95 ( 7454) covalent geometry : angle 1.43461 / 1.12 (10100) hydrogen bonds : bond 0.21944 / 14.42 ( 282) hydrogen bonds : angle 8.59821 / 5.99 ( 786) Misc. bond : bond 0.08773 / 4.40 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 288 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8270 (mt) REVERT: A 141 VAL cc_start: 0.7725 (m) cc_final: 0.7372 (t) REVERT: A 182 SER cc_start: 0.9050 (m) cc_final: 0.8831 (p) REVERT: A 205 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6261 (mtt-85) REVERT: A 246 TYR cc_start: 0.6259 (m-80) cc_final: 0.5972 (m-80) REVERT: A 253 GLN cc_start: 0.6479 (tt0) cc_final: 0.6168 (tp-100) REVERT: A 332 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7174 (mt-10) REVERT: A 477 VAL cc_start: 0.6694 (t) cc_final: 0.6120 (t) REVERT: A 480 ASP cc_start: 0.5249 (m-30) cc_final: 0.4942 (m-30) REVERT: A 504 VAL cc_start: 0.7491 (t) cc_final: 0.7246 (m) REVERT: A 506 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6879 (ttpp) REVERT: A 519 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7389 (tp30) REVERT: A 536 GLU cc_start: 0.6570 (tt0) cc_final: 0.6065 (pm20) REVERT: A 540 SER cc_start: 0.8943 (m) cc_final: 0.8540 (t) REVERT: C 88 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8271 (mt) REVERT: C 141 VAL cc_start: 0.7727 (m) cc_final: 0.7372 (t) REVERT: C 182 SER cc_start: 0.9050 (m) cc_final: 0.8832 (p) REVERT: C 205 ARG cc_start: 0.6614 (mtp85) cc_final: 0.6262 (mtt-85) REVERT: C 224 GLU cc_start: 0.7124 (tt0) cc_final: 0.6917 (mt-10) REVERT: C 246 TYR cc_start: 0.6259 (m-80) cc_final: 0.5974 (m-80) REVERT: C 253 GLN cc_start: 0.6477 (tt0) cc_final: 0.6167 (tp-100) REVERT: C 332 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7171 (mt-10) REVERT: C 477 VAL cc_start: 0.6693 (t) cc_final: 0.6118 (t) REVERT: C 480 ASP cc_start: 0.5243 (m-30) cc_final: 0.4937 (m-30) REVERT: C 504 VAL cc_start: 0.7493 (t) cc_final: 0.7247 (m) REVERT: C 506 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6881 (ttpp) REVERT: C 519 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7389 (tp30) REVERT: C 536 GLU cc_start: 0.6576 (tt0) cc_final: 0.6069 (pm20) REVERT: C 540 SER cc_start: 0.8942 (m) cc_final: 0.8543 (t) outliers start: 18 outliers final: 2 residues processed: 300 average time/residue: 0.0970 time to fit residues: 37.2815 Evaluate side-chains 134 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 82 ASN A 179 GLN A 344 HIS A 413 HIS A 463 HIS A 466 HIS A 488 ASN A 541 ASN C 72 GLN C 82 ASN C 179 GLN C 344 HIS C 413 HIS C 463 HIS C 466 HIS C 488 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.124969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.104940 restraints weight = 8733.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.107526 restraints weight = 6114.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.109446 restraints weight = 4694.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.110768 restraints weight = 3872.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.111796 restraints weight = 3351.000| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7456 Z= 0.161 Angle : 0.604 6.157 10100 Z= 0.330 Chirality : 0.045 0.140 1108 Planarity : 0.004 0.030 1296 Dihedral : 6.763 73.510 1016 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.08 % Allowed : 13.37 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.28), residues: 896 helix: 0.31 (0.28), residues: 344 sheet: -2.00 (0.39), residues: 154 loop : -1.26 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 185 TYR 0.018 0.002 TYR A 161 PHE 0.017 0.002 PHE C 114 TRP 0.010 0.002 TRP A 208 HIS 0.007 0.002 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 7454) covalent geometry : angle 0.60376 / 0.33 (10100) hydrogen bonds : bond 0.05819 / 3.84 ( 282) hydrogen bonds : angle 5.45004 / 3.76 ( 786) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.232 Fit side-chains REVERT: A 267 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8700 (mt) REVERT: A 504 VAL cc_start: 0.8982 (t) cc_final: 0.8759 (m) REVERT: A 506 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7890 (ttmm) REVERT: C 267 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8703 (mt) REVERT: C 403 SER cc_start: 0.8018 (m) cc_final: 0.7811 (t) REVERT: C 504 VAL cc_start: 0.8981 (t) cc_final: 0.8756 (m) REVERT: C 506 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7892 (ttmm) outliers start: 24 outliers final: 8 residues processed: 154 average time/residue: 0.0764 time to fit residues: 15.8996 Evaluate side-chains 91 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [46, 27, 11, 40, 1, 48, 53, 26, 75, 54, 31] chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS A 488 ASN C 463 HIS C 488 ASN C 541 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.121722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.103174 restraints weight = 8750.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.105543 restraints weight = 6200.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.107037 restraints weight = 4811.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.108311 restraints weight = 4016.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.109112 restraints weight = 3483.420| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7456 Z= 0.135 Angle : 0.531 5.458 10100 Z= 0.287 Chirality : 0.043 0.151 1108 Planarity : 0.004 0.036 1296 Dihedral : 6.404 72.146 1012 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.31 % Allowed : 15.17 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.29), residues: 896 helix: 1.11 (0.29), residues: 328 sheet: -1.69 (0.39), residues: 154 loop : -1.01 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 205 TYR 0.018 0.001 TYR C 435 PHE 0.010 0.001 PHE C 183 TRP 0.009 0.001 TRP A 70 HIS 0.018 0.002 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7454) covalent geometry : angle 0.53117 / 0.29 (10100) hydrogen bonds : bond 0.05011 / 3.27 ( 282) hydrogen bonds : angle 4.89532 / 3.32 ( 786) Misc. bond : bond 0.00002 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.265 Fit side-chains REVERT: A 109 GLU cc_start: 0.6572 (tp30) cc_final: 0.6329 (tp30) REVERT: A 267 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8653 (mt) REVERT: A 441 ARG cc_start: 0.7569 (mmp80) cc_final: 0.7307 (mmp80) REVERT: A 504 VAL cc_start: 0.8973 (t) cc_final: 0.8748 (m) REVERT: A 506 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7965 (ttmm) REVERT: C 109 GLU cc_start: 0.6580 (tp30) cc_final: 0.6339 (tp30) REVERT: C 267 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8653 (mt) REVERT: C 441 ARG cc_start: 0.7578 (mmp80) cc_final: 0.7317 (mmp80) REVERT: C 504 VAL cc_start: 0.8973 (t) cc_final: 0.8745 (m) REVERT: C 506 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7964 (ttmm) outliers start: 18 outliers final: 4 residues processed: 107 average time/residue: 0.0967 time to fit residues: 13.5437 Evaluate side-chains 88 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [22, 12, 62, 66, 43, 52, 77, 47, 45, 60, 58] chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN A 312 HIS A 466 HIS C 179 GLN C 312 HIS C 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.111899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.093761 restraints weight = 9162.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.095506 restraints weight = 6838.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.096896 restraints weight = 5528.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.097795 restraints weight = 4714.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.098664 restraints weight = 4205.424| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7456 Z= 0.246 Angle : 0.605 5.553 10100 Z= 0.330 Chirality : 0.047 0.150 1108 Planarity : 0.005 0.042 1296 Dihedral : 6.638 72.584 1008 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.21 % Allowed : 15.42 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.29), residues: 896 helix: 0.62 (0.29), residues: 342 sheet: -1.73 (0.38), residues: 158 loop : -0.93 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 205 TYR 0.013 0.002 TYR C 435 PHE 0.016 0.002 PHE A 226 TRP 0.008 0.001 TRP C 352 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 ( 7454) covalent geometry : angle 0.60484 / 0.33 (10100) hydrogen bonds : bond 0.06299 / 4.09 ( 282) hydrogen bonds : angle 4.92189 / 3.37 ( 786) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.247 Fit side-chains REVERT: A 109 GLU cc_start: 0.6836 (tp30) cc_final: 0.6551 (tp30) REVERT: A 504 VAL cc_start: 0.8998 (t) cc_final: 0.8794 (m) REVERT: A 506 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7981 (ttmm) REVERT: C 109 GLU cc_start: 0.6845 (tp30) cc_final: 0.6563 (tp30) REVERT: C 504 VAL cc_start: 0.8996 (t) cc_final: 0.8791 (m) REVERT: C 506 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7979 (ttmm) outliers start: 25 outliers final: 16 residues processed: 114 average time/residue: 0.0752 time to fit residues: 12.0980 Evaluate side-chains 91 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [66, 48, 20, 9, 63, 28, 19, 6, 76, 47, 60] chunk 66 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN C 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.098723 restraints weight = 8901.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.100897 restraints weight = 6313.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.102139 restraints weight = 4906.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.103539 restraints weight = 4168.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.104487 restraints weight = 3621.678| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7456 Z= 0.120 Angle : 0.509 5.773 10100 Z= 0.274 Chirality : 0.043 0.142 1108 Planarity : 0.004 0.039 1296 Dihedral : 6.003 57.373 1008 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.19 % Allowed : 18.77 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.29), residues: 896 helix: 0.81 (0.29), residues: 342 sheet: -1.70 (0.37), residues: 158 loop : -0.86 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.020 0.001 TYR C 435 PHE 0.006 0.001 PHE A 183 TRP 0.010 0.001 TRP A 208 HIS 0.003 0.001 HIS C 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7454) covalent geometry : angle 0.50940 / 0.27 (10100) hydrogen bonds : bond 0.04643 / 3.03 ( 282) hydrogen bonds : angle 4.55857 / 3.10 ( 786) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.272 Fit side-chains REVERT: A 216 ASP cc_start: 0.8344 (p0) cc_final: 0.8084 (p0) REVERT: A 504 VAL cc_start: 0.8969 (t) cc_final: 0.8764 (m) REVERT: A 506 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7969 (ttmm) REVERT: C 216 ASP cc_start: 0.8362 (p0) cc_final: 0.8108 (p0) REVERT: C 504 VAL cc_start: 0.8962 (t) cc_final: 0.8754 (m) REVERT: C 506 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7967 (ttmm) outliers start: 17 outliers final: 8 residues processed: 88 average time/residue: 0.0770 time to fit residues: 9.5421 Evaluate side-chains 74 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [12, 70, 27, 74, 81, 0, 83, 3, 68, 16, 63] chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.107464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.089491 restraints weight = 9382.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.091233 restraints weight = 7018.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.092521 restraints weight = 5724.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.093186 restraints weight = 4911.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.094018 restraints weight = 4459.608| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 7456 Z= 0.382 Angle : 0.700 6.764 10100 Z= 0.379 Chirality : 0.052 0.180 1108 Planarity : 0.005 0.045 1296 Dihedral : 6.965 70.264 1008 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.34 % Allowed : 19.41 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.29), residues: 896 helix: 0.43 (0.29), residues: 330 sheet: -1.48 (0.40), residues: 158 loop : -0.98 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 69 TYR 0.021 0.003 TYR C 435 PHE 0.017 0.002 PHE A 226 TRP 0.010 0.002 TRP A 352 HIS 0.011 0.002 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00940 / 0.38 ( 7454) covalent geometry : angle 0.70004 / 0.38 (10100) hydrogen bonds : bond 0.07187 / 4.67 ( 282) hydrogen bonds : angle 5.04870 / 3.46 ( 786) Misc. bond : bond 0.00005 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.196 Fit side-chains REVERT: A 504 VAL cc_start: 0.8938 (t) cc_final: 0.8724 (m) REVERT: A 506 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7912 (ttmm) REVERT: C 205 ARG cc_start: 0.7637 (mtt-85) cc_final: 0.7435 (mtp85) REVERT: C 504 VAL cc_start: 0.8936 (t) cc_final: 0.8721 (m) REVERT: C 506 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7915 (ttmm) outliers start: 26 outliers final: 20 residues processed: 97 average time/residue: 0.0752 time to fit residues: 10.1156 Evaluate side-chains 87 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [59, 14, 16, 66, 82, 86, 20, 5, 35, 36, 28] chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.113162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.094984 restraints weight = 9094.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.096894 restraints weight = 6583.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.098388 restraints weight = 5253.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.099343 restraints weight = 4439.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.099926 restraints weight = 3933.206| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7456 Z= 0.153 Angle : 0.541 6.166 10100 Z= 0.292 Chirality : 0.044 0.147 1108 Planarity : 0.004 0.042 1296 Dihedral : 6.328 60.468 1008 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.73 % Allowed : 19.54 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.29), residues: 896 helix: 0.38 (0.29), residues: 344 sheet: -1.48 (0.41), residues: 158 loop : -0.89 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 205 TYR 0.018 0.001 TYR A 435 PHE 0.010 0.001 PHE C 444 TRP 0.011 0.001 TRP C 208 HIS 0.013 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7454) covalent geometry : angle 0.54142 / 0.29 (10100) hydrogen bonds : bond 0.05192 / 3.39 ( 282) hydrogen bonds : angle 4.69782 / 3.20 ( 786) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.219 Fit side-chains REVERT: A 185 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7757 (ptp90) REVERT: A 261 ASN cc_start: 0.6982 (m-40) cc_final: 0.6670 (m-40) REVERT: A 267 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8756 (mt) REVERT: A 504 VAL cc_start: 0.8909 (t) cc_final: 0.8699 (m) REVERT: A 506 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7921 (ttmm) REVERT: C 185 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7744 (ptp90) REVERT: C 205 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.7398 (mtp85) REVERT: C 261 ASN cc_start: 0.6973 (m-40) cc_final: 0.6686 (m-40) REVERT: C 267 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8767 (mt) REVERT: C 504 VAL cc_start: 0.8908 (t) cc_final: 0.8697 (m) REVERT: C 506 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7924 (ttmm) outliers start: 29 outliers final: 21 residues processed: 97 average time/residue: 0.0843 time to fit residues: 11.2283 Evaluate side-chains 94 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [1, 67, 11, 69, 60, 19, 86, 79, 14, 78, 70] chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.095220 restraints weight = 9195.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.096967 restraints weight = 6808.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.098455 restraints weight = 5485.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.099382 restraints weight = 4664.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.100102 restraints weight = 4148.443| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7456 Z= 0.157 Angle : 0.535 5.604 10100 Z= 0.289 Chirality : 0.044 0.148 1108 Planarity : 0.004 0.042 1296 Dihedral : 6.217 59.198 1008 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.60 % Allowed : 20.44 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.29), residues: 896 helix: 0.39 (0.29), residues: 344 sheet: -1.46 (0.40), residues: 168 loop : -0.82 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 205 TYR 0.021 0.002 TYR A 435 PHE 0.009 0.001 PHE A 226 TRP 0.010 0.001 TRP C 208 HIS 0.010 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7454) covalent geometry : angle 0.53504 / 0.29 (10100) hydrogen bonds : bond 0.05131 / 3.36 ( 282) hydrogen bonds : angle 4.64646 / 3.18 ( 786) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.282 Fit side-chains REVERT: A 185 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7738 (ptp90) REVERT: A 261 ASN cc_start: 0.6745 (m-40) cc_final: 0.5887 (t0) REVERT: A 267 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8773 (mt) REVERT: A 504 VAL cc_start: 0.8907 (t) cc_final: 0.8694 (m) REVERT: A 506 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7825 (ttmm) REVERT: C 185 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7759 (ptp90) REVERT: C 205 ARG cc_start: 0.7666 (mtt-85) cc_final: 0.7404 (mtp85) REVERT: C 261 ASN cc_start: 0.6737 (m-40) cc_final: 0.5898 (t0) REVERT: C 267 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8783 (mt) REVERT: C 504 VAL cc_start: 0.8903 (t) cc_final: 0.8688 (m) REVERT: C 506 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7825 (ttmm) outliers start: 28 outliers final: 22 residues processed: 95 average time/residue: 0.0832 time to fit residues: 10.9070 Evaluate side-chains 99 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [66, 26, 83, 46, 78, 47, 45, 13, 30, 55, 35] chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.112896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.094935 restraints weight = 9052.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.096848 restraints weight = 6610.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.098268 restraints weight = 5239.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.099230 restraints weight = 4421.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.100025 restraints weight = 3917.805| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7456 Z= 0.171 Angle : 0.537 5.348 10100 Z= 0.289 Chirality : 0.044 0.153 1108 Planarity : 0.004 0.042 1296 Dihedral : 6.212 59.229 1008 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.60 % Allowed : 20.57 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.29), residues: 896 helix: 0.43 (0.29), residues: 344 sheet: -1.40 (0.40), residues: 168 loop : -0.82 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 205 TYR 0.020 0.002 TYR C 435 PHE 0.010 0.001 PHE A 226 TRP 0.009 0.001 TRP C 208 HIS 0.009 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 7454) covalent geometry : angle 0.53713 / 0.29 (10100) hydrogen bonds : bond 0.05223 / 3.42 ( 282) hydrogen bonds : angle 4.64826 / 3.17 ( 786) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.269 Fit side-chains REVERT: A 185 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7783 (ptp90) REVERT: A 261 ASN cc_start: 0.6738 (m-40) cc_final: 0.5924 (t0) REVERT: A 267 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8767 (mt) REVERT: A 504 VAL cc_start: 0.8896 (t) cc_final: 0.8680 (m) REVERT: A 506 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7815 (ttmm) REVERT: C 185 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7767 (ptp90) REVERT: C 205 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7397 (mtp85) REVERT: C 261 ASN cc_start: 0.6737 (m-40) cc_final: 0.5934 (t0) REVERT: C 267 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8780 (mt) REVERT: C 504 VAL cc_start: 0.8893 (t) cc_final: 0.8676 (m) REVERT: C 506 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7818 (ttmm) outliers start: 28 outliers final: 22 residues processed: 96 average time/residue: 0.0770 time to fit residues: 10.2124 Evaluate side-chains 97 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 463 HIS Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [38, 18, 64, 27, 20, 13, 65, 1, 2, 0, 33] chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.112566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.095008 restraints weight = 9093.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.096818 restraints weight = 6744.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.098157 restraints weight = 5416.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.099085 restraints weight = 4614.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.099731 restraints weight = 4099.951| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7456 Z= 0.187 Angle : 0.545 5.357 10100 Z= 0.293 Chirality : 0.045 0.155 1108 Planarity : 0.004 0.042 1296 Dihedral : 6.249 58.809 1008 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.60 % Allowed : 20.82 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.29), residues: 896 helix: 0.67 (0.30), residues: 330 sheet: -1.39 (0.40), residues: 168 loop : -0.70 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 205 TYR 0.023 0.002 TYR C 435 PHE 0.011 0.001 PHE A 226 TRP 0.009 0.001 TRP C 352 HIS 0.008 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 7454) covalent geometry : angle 0.54533 / 0.29 (10100) hydrogen bonds : bond 0.05357 / 3.51 ( 282) hydrogen bonds : angle 4.66611 / 3.19 ( 786) Misc. bond : bond 0.00019 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.241 Fit side-chains REVERT: A 185 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7803 (ptp90) REVERT: A 261 ASN cc_start: 0.6641 (m-40) cc_final: 0.5891 (t0) REVERT: A 267 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8788 (mt) REVERT: A 504 VAL cc_start: 0.8903 (t) cc_final: 0.8689 (m) REVERT: A 506 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7762 (ttmm) REVERT: C 185 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7799 (ptp90) REVERT: C 205 ARG cc_start: 0.7668 (mtt-85) cc_final: 0.7406 (mtp85) REVERT: C 261 ASN cc_start: 0.6639 (m-40) cc_final: 0.5900 (t0) REVERT: C 267 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8800 (mt) REVERT: C 504 VAL cc_start: 0.8900 (t) cc_final: 0.8683 (m) REVERT: C 506 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7764 (ttmm) outliers start: 28 outliers final: 20 residues processed: 97 average time/residue: 0.0939 time to fit residues: 12.1014 Evaluate side-chains 94 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: [77, 85, 59, 67, 37, 79, 49, 56, 74, 87, 20] chunk 77 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 HIS C 463 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.117185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.098706 restraints weight = 8919.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.100673 restraints weight = 6404.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.102329 restraints weight = 5057.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.103333 restraints weight = 4220.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.104174 restraints weight = 3716.345| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7456 Z= 0.109 Angle : 0.492 5.603 10100 Z= 0.264 Chirality : 0.042 0.142 1108 Planarity : 0.004 0.040 1296 Dihedral : 5.885 56.041 1008 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.83 % Allowed : 22.11 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.29), residues: 896 helix: 0.60 (0.29), residues: 340 sheet: -1.34 (0.40), residues: 168 loop : -0.76 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 205 TYR 0.023 0.001 TYR C 435 PHE 0.008 0.001 PHE A 356 TRP 0.012 0.001 TRP A 208 HIS 0.005 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 7454) covalent geometry : angle 0.49248 / 0.26 (10100) hydrogen bonds : bond 0.04395 / 2.89 ( 282) hydrogen bonds : angle 4.45496 / 3.03 ( 786) Misc. bond : bond 0.00019 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1130.91 seconds wall clock time: 20 minutes 18.27 seconds (1218.27 seconds total)