Starting phenix.real_space_refine on Thu Jul 2 06:19:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn7_52308/07_2026/9hn7_52308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn7_52308/07_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_52308/07_2026/9hn7_52308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn7_52308/07_2026/9hn7_52308.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn7_52308/07_2026/9hn7_52308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn7_52308/07_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-dev-6108/lib/python3.11/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: 1.61, per 1000 atoms: 0.23 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 300.7 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: 0.91 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: 1.17 Time building geometry restraints manager: 0.79 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: 1.780 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.200 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4851 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= 0.196 Angle : 0.569 10.516 10217 Z= 0.297 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/Z covalent geometry : bond 0.00395 / 0.20 ( 7266) covalent geometry : angle 0.56923 / 0.30 (10217) hydrogen bonds : bond 0.16848 / 11.90 ( 273) hydrogen bonds : angle 6.35249 / 4.47 ( 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 : 0.216 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: 0.4139 time to fit residues: 43.3138 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 : 0.214 ------------------------------------------------------------------------------- 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: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.187526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.171200 restraints weight = 20236.116| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 4.10 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7266 Z= 0.139 Angle : 0.630 13.967 10217 Z= 0.318 Chirality : 0.039 0.273 1225 Planarity : 0.004 0.044 1030 Dihedral : 19.619 80.580 1939 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.31 % Allowed : 11.01 % Favored : 86.68 % 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: 0.58 (0.32), residues: 691 helix: 1.35 (0.30), residues: 321 sheet: -0.15 (0.77), residues: 44 loop : -0.46 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 38 TYR 0.024 0.002 TYR A 306 PHE 0.021 0.002 PHE B 141 TRP 0.008 0.001 TRP A 240 HIS 0.009 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7266) covalent geometry : angle 0.63016 / 0.32 (10217) hydrogen bonds : bond 0.06680 / 4.63 ( 273) hydrogen bonds : angle 4.74658 / 3.38 ( 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 90 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.218 Fit side-chains REVERT: A 173 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: A 181 TRP cc_start: 0.7258 (m-10) cc_final: 0.6865 (m-10) REVERT: A 217 MET cc_start: 0.8642 (mpt) cc_final: 0.8091 (mpt) REVERT: A 338 ASN cc_start: 0.3945 (p0) cc_final: 0.3358 (p0) REVERT: A 377 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7239 (mpt) outliers start: 13 outliers final: 4 residues processed: 83 average time/residue: 0.4052 time to fit residues: 35.9096 Evaluate side-chains 78 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN B 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.186140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.168872 restraints weight = 20057.270| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 4.11 r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5182 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7266 Z= 0.137 Angle : 0.610 12.209 10217 Z= 0.312 Chirality : 0.039 0.253 1225 Planarity : 0.004 0.046 1030 Dihedral : 19.582 81.030 1939 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.66 % Allowed : 14.03 % Favored : 83.30 % 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: 1.50 (0.30), residues: 322 sheet: -0.12 (0.68), residues: 49 loop : -0.56 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 121 TYR 0.028 0.002 TYR A 352 PHE 0.018 0.002 PHE A 376 TRP 0.009 0.001 TRP A 240 HIS 0.010 0.001 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 7266) covalent geometry : angle 0.61041 / 0.31 (10217) hydrogen bonds : bond 0.06006 / 4.19 ( 273) hydrogen bonds : angle 4.61767 / 3.32 ( 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 84 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.8615 (mpt) cc_final: 0.8373 (mpt) REVERT: A 338 ASN cc_start: 0.4021 (p0) cc_final: 0.3439 (p0) REVERT: A 377 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7216 (mpt) REVERT: A 379 THR cc_start: 0.8955 (m) cc_final: 0.8730 (p) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 0.3999 time to fit residues: 32.9770 Evaluate side-chains 70 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL 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 363 TYR 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: 0.4980 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN ** B 382 HIS ** 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 = 0.4823 r_free = 0.4823 target = 0.181973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.164367 restraints weight = 20285.194| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 4.14 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7266 Z= 0.187 Angle : 0.675 10.620 10217 Z= 0.347 Chirality : 0.041 0.225 1225 Planarity : 0.006 0.077 1030 Dihedral : 19.676 82.791 1939 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.37 % Allowed : 16.70 % Favored : 79.93 % 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: 0.23 (0.32), residues: 691 helix: 1.16 (0.29), residues: 316 sheet: -0.47 (0.76), residues: 45 loop : -0.71 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 177 TYR 0.034 0.003 TYR A 352 PHE 0.023 0.003 PHE B 141 TRP 0.029 0.003 TRP A 181 HIS 0.008 0.002 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 7266) covalent geometry : angle 0.67546 / 0.35 (10217) hydrogen bonds : bond 0.05984 / 4.29 ( 273) hydrogen bonds : angle 4.84319 / 3.47 ( 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 87 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 CYS cc_start: 0.8879 (m) cc_final: 0.8606 (m) REVERT: A 338 ASN cc_start: 0.4509 (p0) cc_final: 0.3918 (p0) REVERT: A 377 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7226 (mpt) outliers start: 19 outliers final: 9 residues processed: 78 average time/residue: 0.3970 time to fit residues: 33.2443 Evaluate side-chains 76 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 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 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 363 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS ** A 157 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 = 0.4815 r_free = 0.4815 target = 0.181209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.163533 restraints weight = 20184.863| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 4.13 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5445 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7266 Z= 0.179 Angle : 0.686 14.076 10217 Z= 0.343 Chirality : 0.041 0.272 1225 Planarity : 0.005 0.080 1030 Dihedral : 19.791 85.364 1939 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.20 % Allowed : 19.18 % Favored : 77.62 % 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: 0.12 (0.32), residues: 691 helix: 1.13 (0.29), residues: 316 sheet: -0.63 (0.78), residues: 45 loop : -0.82 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 177 TYR 0.028 0.003 TYR A 352 PHE 0.013 0.002 PHE B 141 TRP 0.008 0.002 TRP B 116 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 7266) covalent geometry : angle 0.68558 / 0.34 (10217) hydrogen bonds : bond 0.05897 / 4.22 ( 273) hydrogen bonds : angle 4.83051 / 3.47 ( 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 93 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ASN cc_start: 0.4405 (p0) cc_final: 0.3800 (p0) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.3817 time to fit residues: 35.2636 Evaluate side-chains 77 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 237 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS ** A 157 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 = 0.4821 r_free = 0.4821 target = 0.181697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.164073 restraints weight = 20247.710| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 4.14 r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7266 Z= 0.148 Angle : 0.672 12.564 10217 Z= 0.333 Chirality : 0.042 0.428 1225 Planarity : 0.005 0.079 1030 Dihedral : 19.829 86.721 1939 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.84 % Allowed : 21.49 % Favored : 75.67 % 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: 0.14 (0.32), residues: 691 helix: 1.23 (0.30), residues: 316 sheet: -0.80 (0.70), residues: 47 loop : -0.89 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 177 TYR 0.023 0.002 TYR A 352 PHE 0.019 0.002 PHE A 376 TRP 0.008 0.002 TRP A 181 HIS 0.006 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 7266) covalent geometry : angle 0.67224 / 0.33 (10217) hydrogen bonds : bond 0.05616 / 3.99 ( 273) hydrogen bonds : angle 4.78299 / 3.45 ( 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 83 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ASN cc_start: 0.4169 (p0) cc_final: 0.3604 (p0) REVERT: B 234 HIS cc_start: 0.5441 (OUTLIER) cc_final: 0.5024 (t-90) outliers start: 16 outliers final: 12 residues processed: 77 average time/residue: 0.4337 time to fit residues: 35.6807 Evaluate side-chains 77 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 363 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 126 HIS A 157 GLN A 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.181374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.163739 restraints weight = 20061.177| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 4.13 r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7266 Z= 0.153 Angle : 0.685 10.373 10217 Z= 0.344 Chirality : 0.041 0.358 1225 Planarity : 0.005 0.089 1030 Dihedral : 19.828 88.711 1939 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.20 % Allowed : 21.85 % Favored : 74.96 % 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 (0.32), residues: 691 helix: 1.30 (0.30), residues: 316 sheet: -0.75 (0.70), residues: 47 loop : -0.92 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.032 0.003 TYR A 352 PHE 0.017 0.002 PHE A 376 TRP 0.008 0.002 TRP A 240 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7266) covalent geometry : angle 0.68457 / 0.34 (10217) hydrogen bonds : bond 0.05563 / 3.94 ( 273) hydrogen bonds : angle 4.72656 / 3.40 ( 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 91 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7904 (pp30) REVERT: A 117 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.5058 (mm) REVERT: A 154 ILE cc_start: 0.5006 (OUTLIER) cc_final: 0.4729 (pt) REVERT: A 176 HIS cc_start: 0.7815 (m-70) cc_final: 0.7572 (m-70) REVERT: A 181 TRP cc_start: 0.6976 (m-10) cc_final: 0.6555 (m-10) REVERT: A 338 ASN cc_start: 0.4197 (p0) cc_final: 0.3632 (p0) REVERT: B 38 ARG cc_start: 0.5068 (tpt90) cc_final: 0.4462 (tpt170) REVERT: B 74 LEU cc_start: 0.6893 (mp) cc_final: 0.5690 (tp) REVERT: B 77 TYR cc_start: 0.7404 (t80) cc_final: 0.7083 (t80) REVERT: B 234 HIS cc_start: 0.5446 (OUTLIER) cc_final: 0.5025 (t-90) outliers start: 18 outliers final: 12 residues processed: 84 average time/residue: 0.4374 time to fit residues: 39.3307 Evaluate side-chains 84 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 369 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 126 HIS A 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.182568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.164994 restraints weight = 20324.077| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 4.17 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7266 Z= 0.137 Angle : 0.683 10.132 10217 Z= 0.340 Chirality : 0.042 0.350 1225 Planarity : 0.005 0.080 1030 Dihedral : 19.808 88.532 1939 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.20 % Allowed : 22.74 % Favored : 74.07 % 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: 0.24 (0.32), residues: 691 helix: 1.26 (0.29), residues: 322 sheet: -0.85 (0.73), residues: 44 loop : -0.80 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.035 0.002 TYR A 352 PHE 0.016 0.002 PHE B 274 TRP 0.008 0.001 TRP A 240 HIS 0.006 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7266) covalent geometry : angle 0.68320 / 0.34 (10217) hydrogen bonds : bond 0.05504 / 3.88 ( 273) hydrogen bonds : angle 4.72062 / 3.38 ( 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 90 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5334 (OUTLIER) cc_final: 0.5082 (mm) REVERT: A 154 ILE cc_start: 0.4969 (OUTLIER) cc_final: 0.4678 (pt) REVERT: A 176 HIS cc_start: 0.7786 (m-70) cc_final: 0.7582 (m-70) REVERT: A 338 ASN cc_start: 0.4042 (p0) cc_final: 0.3461 (p0) REVERT: B 234 HIS cc_start: 0.5435 (OUTLIER) cc_final: 0.5013 (t-90) outliers start: 18 outliers final: 10 residues processed: 82 average time/residue: 0.4229 time to fit residues: 37.0491 Evaluate side-chains 79 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 192 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 237 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 126 HIS A 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.183031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.165590 restraints weight = 19927.862| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 4.10 r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7266 Z= 0.140 Angle : 0.728 11.325 10217 Z= 0.358 Chirality : 0.043 0.321 1225 Planarity : 0.005 0.074 1030 Dihedral : 19.778 88.890 1939 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.20 % Allowed : 22.74 % Favored : 74.07 % 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 (0.32), residues: 691 helix: 1.18 (0.29), residues: 322 sheet: -0.68 (0.73), residues: 44 loop : -0.84 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.030 0.003 TYR A 352 PHE 0.015 0.002 PHE A 376 TRP 0.008 0.001 TRP A 240 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7266) covalent geometry : angle 0.72833 / 0.36 (10217) hydrogen bonds : bond 0.05394 / 3.78 ( 273) hydrogen bonds : angle 4.77863 / 3.42 ( 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 87 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.5032 (mm) REVERT: A 154 ILE cc_start: 0.4837 (OUTLIER) cc_final: 0.4547 (pt) REVERT: A 176 HIS cc_start: 0.7789 (m-70) cc_final: 0.7585 (m-70) REVERT: A 338 ASN cc_start: 0.3964 (p0) cc_final: 0.3370 (p0) REVERT: B 74 LEU cc_start: 0.6839 (mp) cc_final: 0.5707 (tp) REVERT: B 234 HIS cc_start: 0.5396 (OUTLIER) cc_final: 0.4970 (t-90) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 0.4407 time to fit residues: 36.7702 Evaluate side-chains 79 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 GLN 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 A residue 379 THR Chi-restraints excluded: chain B residue 37 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 126 HIS A 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.182833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.165315 restraints weight = 20238.380| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 4.14 r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 7266 Z= 0.152 Angle : 0.752 11.668 10217 Z= 0.371 Chirality : 0.044 0.317 1225 Planarity : 0.005 0.075 1030 Dihedral : 19.782 89.273 1939 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.20 % Allowed : 22.56 % Favored : 74.25 % 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: 0.05 (0.31), residues: 691 helix: 1.10 (0.29), residues: 321 sheet: -0.76 (0.71), residues: 44 loop : -0.91 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 80 TYR 0.028 0.002 TYR A 352 PHE 0.013 0.002 PHE B 274 TRP 0.008 0.002 TRP A 240 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7266) covalent geometry : angle 0.75160 / 0.37 (10217) hydrogen bonds : bond 0.05460 / 3.83 ( 273) hydrogen bonds : angle 4.90733 / 3.52 ( 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 84 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.5084 (mm) REVERT: A 154 ILE cc_start: 0.4821 (OUTLIER) cc_final: 0.4539 (pt) REVERT: A 338 ASN cc_start: 0.4061 (p0) cc_final: 0.3456 (p0) REVERT: B 74 LEU cc_start: 0.6887 (mp) cc_final: 0.5773 (tp) REVERT: B 234 HIS cc_start: 0.5403 (OUTLIER) cc_final: 0.4974 (t-90) outliers start: 18 outliers final: 10 residues processed: 76 average time/residue: 0.4658 time to fit residues: 37.8137 Evaluate side-chains 76 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 364 ILE 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 234 HIS Chi-restraints excluded: chain B residue 237 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 126 HIS ** A 157 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 = 0.4813 r_free = 0.4813 target = 0.181407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.163859 restraints weight = 20269.839| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 4.09 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7266 Z= 0.163 Angle : 0.764 11.054 10217 Z= 0.378 Chirality : 0.043 0.296 1225 Planarity : 0.005 0.069 1030 Dihedral : 19.799 91.634 1939 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.84 % Allowed : 22.91 % Favored : 74.25 % 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: 1.01 (0.30), residues: 315 sheet: -0.76 (0.67), residues: 51 loop : -0.97 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 80 TYR 0.027 0.002 TYR A 352 PHE 0.018 0.002 PHE B 170 TRP 0.010 0.002 TRP A 240 HIS 0.010 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 7266) covalent geometry : angle 0.76389 / 0.38 (10217) hydrogen bonds : bond 0.05505 / 3.90 ( 273) hydrogen bonds : angle 5.02178 / 3.63 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.93 seconds wall clock time: 33 minutes 24.31 seconds (2004.31 seconds total)