Starting phenix.real_space_refine on Tue Feb 3 21:27:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn7_52308/02_2026/9hn7_52308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn7_52308/02_2026/9hn7_52308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hn7_52308/02_2026/9hn7_52308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn7_52308/02_2026/9hn7_52308.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn7_52308/02_2026/9hn7_52308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn7_52308/02_2026/9hn7_52308.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 46 5.16 5 C 4114 2.51 5 N 1206 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6962 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2883 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 359} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2455 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 310} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1613 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 27} Link IDs: {'rna2p': 18, 'rna3p': 57} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'9DG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.20 Number of scatterers: 6962 At special positions: 0 Unit cell: (74.76, 84.84, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 76 15.00 O 1520 8.00 N 1206 7.00 C 4114 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=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 225.6 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 51.2% alpha, 8.5% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.780A pdb=" N LEU A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.804A pdb=" N GLY A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.633A pdb=" N SER A 116 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.831A pdb=" N GLU A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 169 through 189 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 235 through 250 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.501A pdb=" N GLU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 4.302A pdb=" N ARG A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.693A pdb=" N PHE B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.806A pdb=" N GLU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.654A pdb=" N ARG B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.724A pdb=" N TYR B 340 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 341 " --> pdb=" O LYS B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.041A pdb=" N HIS B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 370 removed outlier: 3.505A pdb=" N ILE B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 400 removed outlier: 3.739A pdb=" N GLY B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 7.144A pdb=" N MET A 17 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ARG A 34 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 19 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLU A 32 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 21 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.448A pdb=" N VAL A 44 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG A 256 " --> pdb=" O MET A 277 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE A 225 " --> pdb=" O TYR A 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.563A pdb=" N CYS A 70 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ASP A 105 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 72 " --> pdb=" O ASP A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.606A pdb=" N LEU A 138 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 7.410A pdb=" N GLY B 32 " --> pdb=" O PHE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.294A pdb=" N LEU B 35 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR B 63 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR B 37 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 219 Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 286 247 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 986 1.31 - 1.43: 2366 1.43 - 1.56: 3695 1.56 - 1.68: 151 1.68 - 1.81: 68 Bond restraints: 7266 Sorted by residual: bond pdb=" C2 9DG A 501 " pdb=" N3 9DG A 501 " ideal model delta sigma weight residual 1.298 1.464 -0.166 2.00e-02 2.50e+03 6.85e+01 bond pdb=" C4 9DG A 501 " pdb=" N3 9DG A 501 " ideal model delta sigma weight residual 1.363 1.489 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C5 9DG A 501 " pdb=" C6 9DG A 501 " ideal model delta sigma weight residual 1.419 1.530 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C2 9DG A 501 " pdb=" N2 9DG A 501 " ideal model delta sigma weight residual 1.356 1.452 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C2 9DG A 501 " pdb=" N1 9DG A 501 " ideal model delta sigma weight residual 1.371 1.444 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 7261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10091 2.10 - 4.21: 97 4.21 - 6.31: 21 6.31 - 8.41: 5 8.41 - 10.52: 3 Bond angle restraints: 10217 Sorted by residual: angle pdb=" N GLU A 216 " pdb=" CA GLU A 216 " pdb=" CB GLU A 216 " ideal model delta sigma weight residual 110.16 115.83 -5.67 1.48e+00 4.57e-01 1.47e+01 angle pdb=" OP1 G C 34 " pdb=" P G C 34 " pdb=" OP2 G C 34 " ideal model delta sigma weight residual 119.60 109.08 10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" OP1 C C 1 " pdb=" P C C 1 " pdb=" OP2 C C 1 " ideal model delta sigma weight residual 119.60 109.45 10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C5 9DG A 501 " pdb=" C6 9DG A 501 " pdb=" N1 9DG A 501 " ideal model delta sigma weight residual 110.30 119.87 -9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C LYS A 215 " pdb=" N GLU A 216 " pdb=" CA GLU A 216 " ideal model delta sigma weight residual 120.29 115.92 4.37 1.42e+00 4.96e-01 9.46e+00 ... (remaining 10212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 3788 16.07 - 32.14: 354 32.14 - 48.21: 133 48.21 - 64.29: 132 64.29 - 80.36: 32 Dihedral angle restraints: 4439 sinusoidal: 2430 harmonic: 2009 Sorted by residual: dihedral pdb=" CA TYR B 77 " pdb=" C TYR B 77 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO B 104 " pdb=" C PRO B 104 " pdb=" N ALA B 105 " pdb=" CA ALA B 105 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLY A 91 " pdb=" C GLY A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta harmonic sigma weight residual 180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1100 0.055 - 0.109: 110 0.109 - 0.164: 13 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1225 Sorted by residual: chirality pdb=" P G C 34 " pdb=" OP1 G C 34 " pdb=" OP2 G C 34 " pdb=" O5' G C 34 " both_signs ideal model delta sigma weight residual True 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" P C C 1 " pdb=" OP1 C C 1 " pdb=" OP2 C C 1 " pdb=" O5' C C 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO B 102 " pdb=" N PRO B 102 " pdb=" C PRO B 102 " pdb=" CB PRO B 102 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1222 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 82 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 83 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 294 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 295 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 118 " -0.010 2.00e-02 2.50e+03 9.68e-03 1.64e+00 pdb=" CG PHE B 118 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 118 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 118 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 118 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 118 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 118 " -0.000 2.00e-02 2.50e+03 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 657 2.74 - 3.28: 7110 3.28 - 3.82: 13076 3.82 - 4.36: 15010 4.36 - 4.90: 23735 Nonbonded interactions: 59588 Sorted by model distance: nonbonded pdb=" OG SER A 129 " pdb=" O TYR A 131 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 255 " pdb=" OH TYR B 387 " model vdw 2.226 3.040 nonbonded pdb=" O2' A C 9 " pdb=" N7 G C 10 " model vdw 2.236 3.120 nonbonded pdb=" O SER B 255 " pdb=" OH TYR B 387 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A 58 " pdb=" OE1 GLN A 61 " model vdw 2.252 3.040 ... (remaining 59583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.180 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4845 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 : 0.004 0.166 7266 Z= 0.192 Angle : 0.569 10.516 10217 Z= 0.280 Chirality : 0.035 0.273 1225 Planarity : 0.004 0.083 1030 Dihedral : 18.801 80.357 3143 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.68 (0.33), residues: 691 helix: 1.41 (0.31), residues: 318 sheet: -0.17 (0.92), residues: 34 loop : -0.36 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 38 TYR 0.016 0.001 TYR B 77 PHE 0.023 0.001 PHE B 118 TRP 0.010 0.001 TRP A 181 HIS 0.002 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7266) covalent geometry : angle 0.56918 (10217) hydrogen bonds : bond 0.16848 ( 273) hydrogen bonds : angle 6.35249 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8296 (tp30) cc_final: 0.8080 (tp30) REVERT: A 338 ASN cc_start: 0.4182 (p0) cc_final: 0.3443 (p0) REVERT: B 369 MET cc_start: 0.7205 (mmt) cc_final: 0.6981 (mpt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.4173 time to fit residues: 43.4734 Evaluate side-chains 74 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.187338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.170849 restraints weight = 20299.437| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 4.07 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5097 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7266 Z= 0.138 Angle : 0.641 13.744 10217 Z= 0.310 Chirality : 0.038 0.199 1225 Planarity : 0.004 0.041 1030 Dihedral : 19.595 80.646 1939 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.31 % Allowed : 11.37 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.64 (0.32), residues: 691 helix: 1.40 (0.30), residues: 321 sheet: 0.31 (0.87), residues: 34 loop : -0.48 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.016 0.002 TYR A 352 PHE 0.023 0.002 PHE A 376 TRP 0.009 0.001 TRP A 240 HIS 0.009 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7266) covalent geometry : angle 0.64146 (10217) hydrogen bonds : bond 0.05635 ( 273) hydrogen bonds : angle 4.57126 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.7286 (m-10) cc_final: 0.7027 (m-10) REVERT: A 338 ASN cc_start: 0.3922 (p0) cc_final: 0.3406 (p0) REVERT: A 377 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7272 (mpt) REVERT: A 379 THR cc_start: 0.8753 (m) cc_final: 0.8523 (p) REVERT: B 369 MET cc_start: 0.7416 (mmt) cc_final: 0.7206 (mpt) outliers start: 13 outliers final: 5 residues processed: 80 average time/residue: 0.4304 time to fit residues: 36.6468 Evaluate side-chains 77 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** B 133 GLN ** 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 = 0.4870 r_free = 0.4870 target = 0.185732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.168587 restraints weight = 20146.435| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 4.10 r_work (final): 0.4625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5200 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7266 Z= 0.132 Angle : 0.615 11.608 10217 Z= 0.305 Chirality : 0.038 0.219 1225 Planarity : 0.004 0.042 1030 Dihedral : 19.582 82.636 1939 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.31 % Allowed : 13.68 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.65 (0.32), residues: 691 helix: 1.54 (0.30), residues: 321 sheet: -0.45 (0.71), residues: 44 loop : -0.54 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.024 0.002 TYR A 352 PHE 0.023 0.002 PHE A 376 TRP 0.009 0.002 TRP A 240 HIS 0.012 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7266) covalent geometry : angle 0.61537 (10217) hydrogen bonds : bond 0.05020 ( 273) hydrogen bonds : angle 4.49732 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 CYS cc_start: 0.8853 (m) cc_final: 0.8481 (m) REVERT: A 217 MET cc_start: 0.8580 (mpt) cc_final: 0.8370 (mpt) REVERT: A 338 ASN cc_start: 0.3952 (p0) cc_final: 0.3387 (p0) REVERT: A 377 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7242 (mpt) REVERT: A 379 THR cc_start: 0.8961 (m) cc_final: 0.8684 (p) REVERT: B 38 ARG cc_start: 0.4567 (tpt170) cc_final: 0.3941 (tpt90) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.4205 time to fit residues: 35.4999 Evaluate side-chains 74 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 192 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.0370 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.183042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.165491 restraints weight = 20442.307| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 4.11 r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7266 Z= 0.154 Angle : 0.642 10.555 10217 Z= 0.319 Chirality : 0.039 0.205 1225 Planarity : 0.005 0.048 1030 Dihedral : 19.626 85.421 1939 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.73 % Allowed : 14.03 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.50 (0.32), residues: 691 helix: 1.47 (0.30), residues: 316 sheet: -0.72 (0.70), residues: 44 loop : -0.62 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.027 0.002 TYR A 352 PHE 0.019 0.002 PHE A 376 TRP 0.010 0.002 TRP B 116 HIS 0.006 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7266) covalent geometry : angle 0.64192 (10217) hydrogen bonds : bond 0.05078 ( 273) hydrogen bonds : angle 4.61711 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.5254 (OUTLIER) cc_final: 0.4412 (pmm) REVERT: A 181 TRP cc_start: 0.7169 (m-10) cc_final: 0.6780 (m-10) REVERT: A 277 MET cc_start: 0.4284 (mmt) cc_final: 0.4083 (mmt) REVERT: A 338 ASN cc_start: 0.4108 (p0) cc_final: 0.3530 (p0) REVERT: A 352 TYR cc_start: 0.6441 (t80) cc_final: 0.6135 (t80) outliers start: 21 outliers final: 11 residues processed: 81 average time/residue: 0.3886 time to fit residues: 33.7249 Evaluate side-chains 76 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 363 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.171881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.153767 restraints weight = 20288.818| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 4.05 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 7266 Z= 0.343 Angle : 0.956 9.780 10217 Z= 0.477 Chirality : 0.050 0.293 1225 Planarity : 0.007 0.064 1030 Dihedral : 20.277 104.152 1939 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 31.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.09 % Allowed : 19.89 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.83 (0.30), residues: 691 helix: 0.19 (0.28), residues: 310 sheet: -1.17 (0.69), residues: 52 loop : -1.10 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 166 TYR 0.025 0.004 TYR A 352 PHE 0.025 0.004 PHE A 198 TRP 0.013 0.003 TRP A 181 HIS 0.045 0.003 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00762 ( 7266) covalent geometry : angle 0.95583 (10217) hydrogen bonds : bond 0.07716 ( 273) hydrogen bonds : angle 5.77272 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: A 181 TRP cc_start: 0.6993 (m-10) cc_final: 0.6754 (m-10) REVERT: A 380 MET cc_start: 0.7987 (pmm) cc_final: 0.7779 (pmm) REVERT: B 234 HIS cc_start: 0.5567 (OUTLIER) cc_final: 0.5115 (t-90) outliers start: 23 outliers final: 12 residues processed: 95 average time/residue: 0.3706 time to fit residues: 37.6427 Evaluate side-chains 89 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 237 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 63 optimal weight: 0.0370 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 101 ASN A 126 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.179371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.161727 restraints weight = 20434.785| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 4.09 r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7266 Z= 0.153 Angle : 0.738 13.629 10217 Z= 0.362 Chirality : 0.041 0.252 1225 Planarity : 0.005 0.043 1030 Dihedral : 20.103 95.777 1939 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.26 % Allowed : 22.20 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.17 (0.31), residues: 691 helix: 0.86 (0.29), residues: 320 sheet: -1.59 (0.78), residues: 34 loop : -0.88 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 166 TYR 0.024 0.002 TYR A 352 PHE 0.022 0.002 PHE A 369 TRP 0.008 0.002 TRP A 181 HIS 0.013 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7266) covalent geometry : angle 0.73837 (10217) hydrogen bonds : bond 0.05389 ( 273) hydrogen bonds : angle 5.07400 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.5337 (pmm) cc_final: 0.4697 (pmm) REVERT: A 117 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.5350 (mm) REVERT: A 259 MET cc_start: 0.3431 (OUTLIER) cc_final: 0.2922 (pmm) REVERT: A 380 MET cc_start: 0.7881 (pmm) cc_final: 0.7519 (pmm) REVERT: B 234 HIS cc_start: 0.5365 (OUTLIER) cc_final: 0.4692 (t-90) REVERT: B 237 SER cc_start: 0.6809 (t) cc_final: 0.6378 (p) outliers start: 24 outliers final: 13 residues processed: 93 average time/residue: 0.3639 time to fit residues: 36.2925 Evaluate side-chains 86 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 234 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 126 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.173685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.155564 restraints weight = 20488.724| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 4.13 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 7266 Z= 0.272 Angle : 0.875 13.771 10217 Z= 0.429 Chirality : 0.047 0.287 1225 Planarity : 0.006 0.049 1030 Dihedral : 20.268 103.458 1939 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 27.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.26 % Allowed : 22.38 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.60 (0.30), residues: 691 helix: 0.48 (0.28), residues: 313 sheet: -1.24 (0.79), residues: 42 loop : -1.10 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 166 TYR 0.030 0.003 TYR A 352 PHE 0.024 0.003 PHE A 369 TRP 0.012 0.002 TRP A 181 HIS 0.013 0.002 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 7266) covalent geometry : angle 0.87479 (10217) hydrogen bonds : bond 0.06319 ( 273) hydrogen bonds : angle 5.49445 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5545 (mm) REVERT: A 259 MET cc_start: 0.3731 (OUTLIER) cc_final: 0.3522 (pmm) REVERT: A 308 LYS cc_start: 0.5767 (tppt) cc_final: 0.5365 (mmmt) REVERT: B 234 HIS cc_start: 0.5525 (OUTLIER) cc_final: 0.5039 (t-90) outliers start: 24 outliers final: 10 residues processed: 96 average time/residue: 0.3629 time to fit residues: 37.2955 Evaluate side-chains 87 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 234 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 157 GLN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.177863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.160142 restraints weight = 20671.465| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 4.12 r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7266 Z= 0.157 Angle : 0.773 14.980 10217 Z= 0.376 Chirality : 0.043 0.286 1225 Planarity : 0.005 0.043 1030 Dihedral : 20.244 100.447 1939 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.37 % Allowed : 23.98 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.21 (0.32), residues: 691 helix: 0.73 (0.29), residues: 321 sheet: -0.73 (0.73), residues: 48 loop : -0.89 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 80 TYR 0.028 0.003 TYR A 352 PHE 0.019 0.002 PHE A 329 TRP 0.014 0.002 TRP A 181 HIS 0.011 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7266) covalent geometry : angle 0.77349 (10217) hydrogen bonds : bond 0.05351 ( 273) hydrogen bonds : angle 5.14165 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.3814 (OUTLIER) cc_final: 0.2782 (pmm) REVERT: B 74 LEU cc_start: 0.6800 (mp) cc_final: 0.5892 (tp) REVERT: B 77 TYR cc_start: 0.7633 (t80) cc_final: 0.7389 (t80) REVERT: B 136 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6064 (tp) REVERT: B 234 HIS cc_start: 0.5368 (OUTLIER) cc_final: 0.4864 (t-90) REVERT: B 369 MET cc_start: 0.7743 (mmp) cc_final: 0.7280 (mpm) outliers start: 19 outliers final: 10 residues processed: 99 average time/residue: 0.3145 time to fit residues: 33.5092 Evaluate side-chains 91 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 234 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 157 GLN A 238 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.178956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.161369 restraints weight = 20121.910| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 4.04 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7266 Z= 0.151 Angle : 0.786 13.528 10217 Z= 0.379 Chirality : 0.044 0.401 1225 Planarity : 0.005 0.041 1030 Dihedral : 20.198 101.500 1939 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.20 % Allowed : 25.22 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.08 (0.32), residues: 691 helix: 0.83 (0.29), residues: 321 sheet: -0.42 (0.73), residues: 48 loop : -0.87 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 166 TYR 0.030 0.002 TYR A 352 PHE 0.017 0.002 PHE A 369 TRP 0.015 0.002 TRP A 240 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7266) covalent geometry : angle 0.78551 (10217) hydrogen bonds : bond 0.05140 ( 273) hydrogen bonds : angle 5.10036 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.1513 (OUTLIER) cc_final: 0.1237 (t) REVERT: A 238 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: A 259 MET cc_start: 0.3645 (OUTLIER) cc_final: 0.3068 (pmm) REVERT: B 74 LEU cc_start: 0.6802 (mp) cc_final: 0.5870 (tp) REVERT: B 77 TYR cc_start: 0.7639 (t80) cc_final: 0.7329 (t80) REVERT: B 136 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.6084 (tp) REVERT: B 192 VAL cc_start: 0.5338 (m) cc_final: 0.5132 (t) REVERT: B 234 HIS cc_start: 0.5409 (OUTLIER) cc_final: 0.4916 (t-90) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.4575 time to fit residues: 45.4618 Evaluate side-chains 95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 234 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 157 GLN A 238 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.179766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.162072 restraints weight = 20348.410| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 4.12 r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7266 Z= 0.152 Angle : 0.794 16.346 10217 Z= 0.383 Chirality : 0.042 0.276 1225 Planarity : 0.004 0.041 1030 Dihedral : 20.181 101.013 1939 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.84 % Allowed : 25.22 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.09 (0.32), residues: 691 helix: 0.83 (0.29), residues: 321 sheet: -0.34 (0.75), residues: 48 loop : -0.90 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 166 TYR 0.029 0.002 TYR A 352 PHE 0.017 0.002 PHE B 170 TRP 0.013 0.002 TRP A 240 HIS 0.008 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7266) covalent geometry : angle 0.79387 (10217) hydrogen bonds : bond 0.05118 ( 273) hydrogen bonds : angle 5.09180 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.4267 (pmm) cc_final: 0.3820 (pmm) REVERT: A 238 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: A 259 MET cc_start: 0.3760 (OUTLIER) cc_final: 0.2929 (pmm) REVERT: B 74 LEU cc_start: 0.6918 (mp) cc_final: 0.6003 (tp) REVERT: B 77 TYR cc_start: 0.7579 (t80) cc_final: 0.7280 (t80) REVERT: B 136 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6099 (tp) REVERT: B 192 VAL cc_start: 0.5387 (m) cc_final: 0.5152 (t) REVERT: B 234 HIS cc_start: 0.5475 (OUTLIER) cc_final: 0.4997 (t-90) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.4516 time to fit residues: 42.9325 Evaluate side-chains 92 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 234 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 157 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.180111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.162472 restraints weight = 20116.177| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 4.06 r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7266 Z= 0.150 Angle : 0.788 13.713 10217 Z= 0.381 Chirality : 0.044 0.423 1225 Planarity : 0.005 0.041 1030 Dihedral : 20.169 100.415 1939 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.49 % Allowed : 25.58 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.01 (0.32), residues: 691 helix: 0.93 (0.29), residues: 321 sheet: -0.21 (0.76), residues: 48 loop : -0.91 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 166 TYR 0.026 0.002 TYR A 352 PHE 0.018 0.002 PHE B 170 TRP 0.018 0.002 TRP A 240 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7266) covalent geometry : angle 0.78793 (10217) hydrogen bonds : bond 0.05112 ( 273) hydrogen bonds : angle 5.08028 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.57 seconds wall clock time: 32 minutes 35.97 seconds (1955.97 seconds total)