Starting phenix.real_space_refine on Sat May 2 12:44:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uw4_64545/05_2026/9uw4_64545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uw4_64545/05_2026/9uw4_64545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uw4_64545/05_2026/9uw4_64545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uw4_64545/05_2026/9uw4_64545.map" model { file = "/net/cci-nas-00/data/ceres_data/9uw4_64545/05_2026/9uw4_64545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uw4_64545/05_2026/9uw4_64545.cif" } resolution = 3.2 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= 0.116 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 3350 2.51 5 N 899 2.21 5 O 981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5269 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2383 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.28, per 1000 atoms: 0.24 Number of scatterers: 5269 At special positions: 0 Unit cell: (64.133, 81.525, 100.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 8 15.00 Mg 1 11.99 O 981 8.00 N 899 7.00 C 3350 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: 0.45 Conformation dependent library (CDL) restraints added in 205.4 milliseconds 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 40.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 139 through 160 removed outlier: 4.003A pdb=" N ALA B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 removed outlier: 3.795A pdb=" N TRP B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 262 removed outlier: 3.720A pdb=" N ILE B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.649A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.546A pdb=" N GLU B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 3.603A pdb=" N LYS B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.909A pdb=" N GLN A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 162 through 184 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.609A pdb=" N ILE A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.911A pdb=" N VAL A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 370 through 375 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 47 removed outlier: 4.396A pdb=" N LEU B 45 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 58 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 105 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.884A pdb=" N LYS A 84 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU A 73 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL A 82 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 81 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 94 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TYR A 134 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 140 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A 132 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 142 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.514A pdb=" N GLY A 213 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 198 190 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 868 1.32 - 1.45: 1370 1.45 - 1.57: 3086 1.57 - 1.70: 12 1.70 - 1.83: 50 Bond restraints: 5386 Sorted by residual: bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" N3B ANP A 501 " pdb=" PG ANP A 501 " ideal model delta sigma weight residual 1.795 1.637 0.158 2.00e-02 2.50e+03 6.20e+01 bond pdb=" O3P SEP A 222 " pdb=" P SEP A 222 " ideal model delta sigma weight residual 1.610 1.491 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" O3A ANP A 501 " pdb=" PB ANP A 501 " ideal model delta sigma weight residual 1.700 1.585 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" O2P SEP A 222 " pdb=" P SEP A 222 " ideal model delta sigma weight residual 1.610 1.500 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 5381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 7131 2.27 - 4.53: 123 4.53 - 6.80: 26 6.80 - 9.07: 9 9.07 - 11.33: 6 Bond angle restraints: 7295 Sorted by residual: angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 112.38 107.16 5.22 1.22e+00 6.72e-01 1.83e+01 angle pdb=" CB MET B 350 " pdb=" CG MET B 350 " pdb=" SD MET B 350 " ideal model delta sigma weight residual 112.70 124.03 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O1G ANP B 402 " pdb=" PG ANP B 402 " pdb=" O2G ANP B 402 " ideal model delta sigma weight residual 114.42 103.85 10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O ASP A 217 " pdb=" C ASP A 217 " pdb=" N SEP A 218 " ideal model delta sigma weight residual 123.00 117.65 5.35 1.60e+00 3.91e-01 1.12e+01 angle pdb=" N3B ANP A 501 " pdb=" PG ANP A 501 " pdb=" O2G ANP A 501 " ideal model delta sigma weight residual 101.05 110.93 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 7290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 3066 30.52 - 61.04: 220 61.04 - 91.55: 22 91.55 - 122.07: 5 122.07 - 152.59: 2 Dihedral angle restraints: 3315 sinusoidal: 1414 harmonic: 1901 Sorted by residual: dihedral pdb=" O1A ANP A 501 " pdb=" O3A ANP A 501 " pdb=" PA ANP A 501 " pdb=" PB ANP A 501 " ideal model delta sinusoidal sigma weight residual 83.11 -69.48 152.59 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" O1B ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PB ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sinusoidal sigma weight residual 35.15 168.71 -133.56 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" O1B ANP A 501 " pdb=" N3B ANP A 501 " pdb=" PB ANP A 501 " pdb=" PG ANP A 501 " ideal model delta sinusoidal sigma weight residual 35.15 -82.88 118.03 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 3312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 741 0.085 - 0.170: 56 0.170 - 0.256: 2 0.256 - 0.341: 1 0.341 - 0.426: 1 Chirality restraints: 801 Sorted by residual: chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.78 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C3' ANP A 501 " pdb=" C2' ANP A 501 " pdb=" C4' ANP A 501 " pdb=" O3' ANP A 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA SEP A 218 " pdb=" N SEP A 218 " pdb=" C SEP A 218 " pdb=" CB SEP A 218 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 798 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SEP A 218 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SEP A 218 " 0.064 2.00e-02 2.50e+03 pdb=" O SEP A 218 " -0.024 2.00e-02 2.50e+03 pdb=" N MET A 219 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP B 402 " -0.024 2.00e-02 2.50e+03 1.15e-02 3.66e+00 pdb=" C2 ANP B 402 " 0.002 2.00e-02 2.50e+03 pdb=" C4 ANP B 402 " -0.004 2.00e-02 2.50e+03 pdb=" C5 ANP B 402 " 0.002 2.00e-02 2.50e+03 pdb=" C6 ANP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C8 ANP B 402 " 0.002 2.00e-02 2.50e+03 pdb=" N1 ANP B 402 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ANP B 402 " 0.008 2.00e-02 2.50e+03 pdb=" N6 ANP B 402 " -0.006 2.00e-02 2.50e+03 pdb=" N7 ANP B 402 " -0.003 2.00e-02 2.50e+03 pdb=" N9 ANP B 402 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP A 501 " -0.023 2.00e-02 2.50e+03 1.05e-02 3.02e+00 pdb=" C2 ANP A 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 ANP A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C5 ANP A 501 " 0.004 2.00e-02 2.50e+03 pdb=" C6 ANP A 501 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ANP A 501 " -0.002 2.00e-02 2.50e+03 pdb=" N1 ANP A 501 " -0.007 2.00e-02 2.50e+03 pdb=" N3 ANP A 501 " 0.000 2.00e-02 2.50e+03 pdb=" N6 ANP A 501 " -0.013 2.00e-02 2.50e+03 pdb=" N7 ANP A 501 " 0.007 2.00e-02 2.50e+03 pdb=" N9 ANP A 501 " 0.016 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 16 2.58 - 3.16: 4047 3.16 - 3.74: 7671 3.74 - 4.32: 10445 4.32 - 4.90: 17884 Nonbonded interactions: 40063 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O2B ANP B 402 " model vdw 2.000 2.170 nonbonded pdb=" OD2 ASP B 184 " pdb="MG MG B 401 " model vdw 2.042 2.170 nonbonded pdb=" OD1 ASN B 171 " pdb="MG MG B 401 " model vdw 2.072 2.170 nonbonded pdb=" O THR A 226 " pdb=" CG MET A 230 " model vdw 2.351 3.440 nonbonded pdb=" O GLU A 233 " pdb=" OG1 THR A 238 " model vdw 2.381 3.040 ... (remaining 40058 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.720 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.007 0.175 5386 Z= 0.347 Angle : 0.778 11.334 7295 Z= 0.372 Chirality : 0.047 0.426 801 Planarity : 0.004 0.037 924 Dihedral : 20.265 152.591 2087 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 28.70 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.34), residues: 636 helix: 0.59 (0.35), residues: 249 sheet: -0.14 (0.65), residues: 70 loop : -1.74 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 309 TYR 0.014 0.001 TYR B 130 PHE 0.007 0.001 PHE B 200 TRP 0.008 0.001 TRP A 374 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 5386) covalent geometry : angle 0.77780 ( 7295) hydrogen bonds : bond 0.15385 ( 190) hydrogen bonds : angle 5.96323 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.195 Fit side-chains REVERT: B 55 MET cc_start: 0.7945 (tmm) cc_final: 0.7494 (tmm) REVERT: B 105 ASP cc_start: 0.7346 (t70) cc_final: 0.7097 (t70) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0670 time to fit residues: 7.7100 Evaluate side-chains 74 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.159844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130980 restraints weight = 6367.231| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.48 r_work: 0.3408 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5386 Z= 0.206 Angle : 0.593 6.612 7295 Z= 0.296 Chirality : 0.043 0.132 801 Planarity : 0.004 0.036 924 Dihedral : 13.272 132.727 776 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.23 % Allowed : 25.88 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.34), residues: 636 helix: 0.56 (0.35), residues: 253 sheet: 0.09 (0.71), residues: 60 loop : -1.95 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.016 0.002 TYR A 240 PHE 0.012 0.002 PHE A 311 TRP 0.014 0.002 TRP A 374 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 5386) covalent geometry : angle 0.59305 ( 7295) hydrogen bonds : bond 0.04140 ( 190) hydrogen bonds : angle 4.67394 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.198 Fit side-chains REVERT: B 36 PHE cc_start: 0.8434 (t80) cc_final: 0.8186 (t80) REVERT: B 55 MET cc_start: 0.8032 (tmm) cc_final: 0.6904 (tmm) REVERT: B 62 HIS cc_start: 0.7774 (m-70) cc_final: 0.7549 (m-70) REVERT: B 331 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7639 (pt0) outliers start: 24 outliers final: 14 residues processed: 94 average time/residue: 0.0686 time to fit residues: 8.7209 Evaluate side-chains 83 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.0270 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.163103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134591 restraints weight = 6286.477| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.46 r_work: 0.3452 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5386 Z= 0.107 Angle : 0.517 6.007 7295 Z= 0.257 Chirality : 0.041 0.141 801 Planarity : 0.004 0.033 924 Dihedral : 11.665 126.952 776 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.35 % Allowed : 27.46 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.34), residues: 636 helix: 0.88 (0.36), residues: 251 sheet: -0.18 (0.62), residues: 70 loop : -1.87 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.010 0.001 TYR B 156 PHE 0.013 0.001 PHE B 371 TRP 0.007 0.001 TRP A 374 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5386) covalent geometry : angle 0.51682 ( 7295) hydrogen bonds : bond 0.03198 ( 190) hydrogen bonds : angle 4.18417 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.207 Fit side-chains REVERT: B 55 MET cc_start: 0.7729 (tmm) cc_final: 0.6716 (tmm) REVERT: A 138 GLU cc_start: 0.6273 (mm-30) cc_final: 0.6028 (mm-30) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.0664 time to fit residues: 7.9627 Evaluate side-chains 81 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.0050 chunk 54 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134195 restraints weight = 6255.537| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.47 r_work: 0.3450 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5386 Z= 0.110 Angle : 0.499 6.052 7295 Z= 0.248 Chirality : 0.040 0.129 801 Planarity : 0.004 0.032 924 Dihedral : 10.751 122.719 776 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.52 % Allowed : 27.64 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.34), residues: 636 helix: 0.92 (0.36), residues: 252 sheet: -0.20 (0.62), residues: 70 loop : -1.86 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.011 0.001 TYR B 156 PHE 0.009 0.001 PHE A 311 TRP 0.007 0.001 TRP A 374 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5386) covalent geometry : angle 0.49931 ( 7295) hydrogen bonds : bond 0.03013 ( 190) hydrogen bonds : angle 3.97511 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.212 Fit side-chains REVERT: B 55 MET cc_start: 0.7814 (tmm) cc_final: 0.7008 (tmm) REVERT: B 105 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7017 (t70) REVERT: A 138 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5900 (mm-30) outliers start: 20 outliers final: 13 residues processed: 85 average time/residue: 0.0652 time to fit residues: 7.5923 Evaluate side-chains 77 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.160689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131671 restraints weight = 6412.136| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.51 r_work: 0.3413 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5386 Z= 0.146 Angle : 0.534 6.021 7295 Z= 0.267 Chirality : 0.041 0.126 801 Planarity : 0.004 0.035 924 Dihedral : 10.521 124.821 776 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.52 % Allowed : 28.52 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.34), residues: 636 helix: 0.86 (0.35), residues: 252 sheet: -0.19 (0.62), residues: 70 loop : -1.90 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.013 0.001 TYR B 156 PHE 0.013 0.001 PHE B 371 TRP 0.006 0.001 TRP A 374 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5386) covalent geometry : angle 0.53386 ( 7295) hydrogen bonds : bond 0.03361 ( 190) hydrogen bonds : angle 4.02217 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.212 Fit side-chains REVERT: B 55 MET cc_start: 0.7886 (tmm) cc_final: 0.6999 (tmm) REVERT: B 105 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7095 (t70) REVERT: B 366 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 136 ASP cc_start: 0.6154 (t0) cc_final: 0.5832 (t0) REVERT: A 138 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5921 (mm-30) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.0613 time to fit residues: 7.2840 Evaluate side-chains 82 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.0010 chunk 40 optimal weight: 0.0000 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135710 restraints weight = 6307.944| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.49 r_work: 0.3465 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5386 Z= 0.092 Angle : 0.482 6.909 7295 Z= 0.240 Chirality : 0.040 0.127 801 Planarity : 0.003 0.031 924 Dihedral : 10.071 125.738 776 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.17 % Allowed : 28.35 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.34), residues: 636 helix: 1.03 (0.36), residues: 252 sheet: -0.24 (0.61), residues: 70 loop : -1.81 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.008 0.001 TYR B 156 PHE 0.009 0.001 PHE A 311 TRP 0.004 0.001 TRP A 374 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5386) covalent geometry : angle 0.48210 ( 7295) hydrogen bonds : bond 0.02701 ( 190) hydrogen bonds : angle 3.72867 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.199 Fit side-chains REVERT: B 55 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.6909 (tmm) REVERT: B 105 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6996 (t70) REVERT: B 366 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 136 ASP cc_start: 0.6237 (t0) cc_final: 0.5927 (t0) REVERT: A 138 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5808 (mm-30) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.0649 time to fit residues: 7.7105 Evaluate side-chains 81 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131118 restraints weight = 6352.609| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.49 r_work: 0.3404 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5386 Z= 0.155 Angle : 0.540 6.327 7295 Z= 0.268 Chirality : 0.042 0.124 801 Planarity : 0.004 0.034 924 Dihedral : 10.241 128.383 776 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.40 % Allowed : 27.99 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.34), residues: 636 helix: 0.93 (0.35), residues: 252 sheet: -0.16 (0.62), residues: 70 loop : -1.85 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.014 0.001 TYR B 156 PHE 0.013 0.001 PHE B 371 TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5386) covalent geometry : angle 0.53954 ( 7295) hydrogen bonds : bond 0.03344 ( 190) hydrogen bonds : angle 3.94037 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.157 Fit side-chains REVERT: B 105 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7080 (t70) REVERT: B 117 ASP cc_start: 0.8376 (p0) cc_final: 0.8044 (p0) REVERT: B 366 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 102 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: A 136 ASP cc_start: 0.6304 (t0) cc_final: 0.6084 (t0) outliers start: 25 outliers final: 18 residues processed: 91 average time/residue: 0.0615 time to fit residues: 7.7524 Evaluate side-chains 83 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.160613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131472 restraints weight = 6407.495| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.53 r_work: 0.3386 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5386 Z= 0.192 Angle : 0.583 9.035 7295 Z= 0.287 Chirality : 0.043 0.125 801 Planarity : 0.004 0.037 924 Dihedral : 10.418 130.198 776 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 4.23 % Allowed : 27.64 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.34), residues: 636 helix: 0.82 (0.35), residues: 251 sheet: -0.11 (0.63), residues: 70 loop : -1.90 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.018 0.002 TYR A 240 PHE 0.013 0.002 PHE A 311 TRP 0.008 0.002 TRP A 247 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5386) covalent geometry : angle 0.58310 ( 7295) hydrogen bonds : bond 0.03610 ( 190) hydrogen bonds : angle 4.08191 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.207 Fit side-chains REVERT: B 55 MET cc_start: 0.7922 (tmm) cc_final: 0.6853 (tmm) REVERT: B 105 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7139 (t70) REVERT: B 251 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 331 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: B 366 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 102 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: A 136 ASP cc_start: 0.6387 (t0) cc_final: 0.6172 (t0) REVERT: A 354 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6542 (mt0) outliers start: 24 outliers final: 16 residues processed: 86 average time/residue: 0.0647 time to fit residues: 7.6741 Evaluate side-chains 85 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.164276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135153 restraints weight = 6427.232| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.56 r_work: 0.3450 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5386 Z= 0.094 Angle : 0.512 8.308 7295 Z= 0.250 Chirality : 0.040 0.128 801 Planarity : 0.004 0.033 924 Dihedral : 10.115 129.927 776 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.82 % Allowed : 29.23 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.34), residues: 636 helix: 1.07 (0.36), residues: 252 sheet: 0.04 (0.66), residues: 65 loop : -1.82 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.008 0.001 TYR B 156 PHE 0.010 0.001 PHE A 311 TRP 0.005 0.001 TRP A 374 HIS 0.001 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 5386) covalent geometry : angle 0.51215 ( 7295) hydrogen bonds : bond 0.02776 ( 190) hydrogen bonds : angle 3.69545 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.205 Fit side-chains REVERT: B 55 MET cc_start: 0.7738 (tmm) cc_final: 0.6901 (tmm) REVERT: B 105 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6980 (t70) REVERT: B 117 ASP cc_start: 0.8356 (p0) cc_final: 0.8097 (p0) REVERT: B 251 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7573 (mp) REVERT: B 366 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 138 GLU cc_start: 0.6376 (mm-30) cc_final: 0.5620 (mm-30) REVERT: A 354 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6515 (mt0) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.0622 time to fit residues: 6.8880 Evaluate side-chains 78 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134465 restraints weight = 6364.250| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.52 r_work: 0.3450 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5386 Z= 0.104 Angle : 0.538 11.159 7295 Z= 0.263 Chirality : 0.040 0.127 801 Planarity : 0.004 0.032 924 Dihedral : 10.032 129.513 776 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.64 % Allowed : 29.05 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.34), residues: 636 helix: 1.14 (0.36), residues: 252 sheet: -0.10 (0.62), residues: 70 loop : -1.76 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.010 0.001 TYR B 156 PHE 0.009 0.001 PHE A 311 TRP 0.005 0.001 TRP A 374 HIS 0.002 0.000 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5386) covalent geometry : angle 0.53756 ( 7295) hydrogen bonds : bond 0.02747 ( 190) hydrogen bonds : angle 3.64053 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1272 Ramachandran restraints generated. 636 Oldfield, 0 Emsley, 636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.196 Fit side-chains REVERT: B 55 MET cc_start: 0.7733 (tmm) cc_final: 0.6915 (tmm) REVERT: B 105 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7035 (t70) REVERT: B 117 ASP cc_start: 0.8334 (p0) cc_final: 0.8045 (p0) REVERT: B 251 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 366 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 354 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6685 (mt0) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.0641 time to fit residues: 6.6510 Evaluate side-chains 77 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134865 restraints weight = 6355.664| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.53 r_work: 0.3449 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5386 Z= 0.103 Angle : 0.524 8.172 7295 Z= 0.258 Chirality : 0.040 0.127 801 Planarity : 0.004 0.032 924 Dihedral : 9.959 128.959 776 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.64 % Allowed : 29.05 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.34), residues: 636 helix: 1.17 (0.36), residues: 252 sheet: -0.05 (0.63), residues: 70 loop : -1.75 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.010 0.001 TYR B 156 PHE 0.009 0.001 PHE A 311 TRP 0.005 0.001 TRP A 374 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5386) covalent geometry : angle 0.52377 ( 7295) hydrogen bonds : bond 0.02732 ( 190) hydrogen bonds : angle 3.61192 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1171.99 seconds wall clock time: 20 minutes 56.65 seconds (1256.65 seconds total)