Starting phenix.real_space_refine on Tue Jan 13 15:04:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bym_16328/01_2026/8bym_16328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bym_16328/01_2026/8bym_16328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bym_16328/01_2026/8bym_16328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bym_16328/01_2026/8bym_16328.map" model { file = "/net/cci-nas-00/data/ceres_data/8bym_16328/01_2026/8bym_16328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bym_16328/01_2026/8bym_16328.cif" } resolution = 3.15 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 4569 2.51 5 N 1320 2.21 5 O 1488 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-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7386 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2462 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 2, 'TRANS': 318} Chain: "B" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2462 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 2, 'TRANS': 318} Chain: "C" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2462 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 2, 'TRANS': 318} Time building chain proxies: 1.95, per 1000 atoms: 0.26 Number of scatterers: 7386 At special positions: 0 Unit cell: (95.858, 92.414, 84.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 1488 8.00 N 1320 7.00 C 4569 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: 0.49 Conformation dependent library (CDL) restraints added in 286.1 milliseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 6.1% alpha, 56.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.144A pdb=" N GLY A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.861A pdb=" N ALA A 243 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.855A pdb=" N LEU B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 4.071A pdb=" N ALA B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.980A pdb=" N ALA C 243 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 130 removed outlier: 6.750A pdb=" N THR A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 185 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A 167 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE A 183 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 23.968A pdb=" N THR A 182 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 18.593A pdb=" N THR A 206 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 12.712A pdb=" N ASP A 184 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN A 204 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS A 376 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER A 400 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 130 removed outlier: 6.697A pdb=" N THR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 185 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS B 167 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE B 183 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASN B 169 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA B 181 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 23.883A pdb=" N THR B 182 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 18.614A pdb=" N THR B 206 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 12.640A pdb=" N ASP B 184 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN B 204 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 376 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER B 400 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283 Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 130 removed outlier: 6.651A pdb=" N GLN C 161 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL C 188 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL C 163 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 186 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG C 165 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 23.840A pdb=" N THR C 182 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 18.486A pdb=" N THR C 206 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 12.776A pdb=" N ASP C 184 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN C 204 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS C 376 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 400 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 279 through 283 461 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2532 1.34 - 1.46: 1373 1.46 - 1.57: 3598 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 7521 Sorted by residual: bond pdb=" CA ASN B 305 " pdb=" CB ASN B 305 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.61e-02 3.86e+03 1.33e+00 bond pdb=" C TYR A 396 " pdb=" N GLY A 397 " ideal model delta sigma weight residual 1.332 1.328 0.004 5.00e-03 4.00e+04 7.47e-01 bond pdb=" CA ASN B 321 " pdb=" CB ASN B 321 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.55e-01 bond pdb=" C LYS B 304 " pdb=" N ASN B 305 " ideal model delta sigma weight residual 1.328 1.337 -0.010 1.30e-02 5.92e+03 5.37e-01 bond pdb=" CA ASP A 367 " pdb=" CB ASP A 367 " ideal model delta sigma weight residual 1.522 1.531 -0.009 1.27e-02 6.20e+03 5.25e-01 ... (remaining 7516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 9758 1.13 - 2.25: 320 2.25 - 3.38: 50 3.38 - 4.50: 9 4.50 - 5.63: 3 Bond angle restraints: 10140 Sorted by residual: angle pdb=" N ASP A 367 " pdb=" CA ASP A 367 " pdb=" C ASP A 367 " ideal model delta sigma weight residual 107.32 112.95 -5.63 1.65e+00 3.67e-01 1.16e+01 angle pdb=" C LYS A 265 " pdb=" N GLU A 266 " pdb=" CA GLU A 266 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.57e+00 angle pdb=" C ASP B 320 " pdb=" N ASN B 321 " pdb=" CA ASN B 321 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.13e+00 angle pdb=" C LYS B 304 " pdb=" N ASN B 305 " pdb=" CA ASN B 305 " ideal model delta sigma weight residual 122.82 126.54 -3.72 1.42e+00 4.96e-01 6.87e+00 angle pdb=" N GLU C 266 " pdb=" CA GLU C 266 " pdb=" C GLU C 266 " ideal model delta sigma weight residual 114.56 111.30 3.26 1.27e+00 6.20e-01 6.59e+00 ... (remaining 10135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4048 17.88 - 35.76: 250 35.76 - 53.64: 44 53.64 - 71.52: 13 71.52 - 89.40: 7 Dihedral angle restraints: 4362 sinusoidal: 1662 harmonic: 2700 Sorted by residual: dihedral pdb=" CA ASP A 363 " pdb=" CB ASP A 363 " pdb=" CG ASP A 363 " pdb=" OD1 ASP A 363 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB GLU A 415 " pdb=" CG GLU A 415 " pdb=" CD GLU A 415 " pdb=" OE1 GLU A 415 " ideal model delta sinusoidal sigma weight residual 0.00 89.40 -89.40 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP C 363 " pdb=" CB ASP C 363 " pdb=" CG ASP C 363 " pdb=" OD1 ASP C 363 " ideal model delta sinusoidal sigma weight residual -30.00 -82.91 52.91 1 2.00e+01 2.50e-03 9.53e+00 ... (remaining 4359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 621 0.034 - 0.067: 302 0.067 - 0.101: 63 0.101 - 0.135: 44 0.135 - 0.168: 2 Chirality restraints: 1032 Sorted by residual: chirality pdb=" CA ASN B 305 " pdb=" N ASN B 305 " pdb=" C ASN B 305 " pdb=" CB ASN B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ASN B 321 " pdb=" N ASN B 321 " pdb=" C ASN B 321 " pdb=" CB ASN B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA VAL C 382 " pdb=" N VAL C 382 " pdb=" C VAL C 382 " pdb=" CB VAL C 382 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1029 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 215 " -0.004 2.00e-02 2.50e+03 9.17e-03 8.41e-01 pdb=" CG ASP A 215 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASP A 215 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP A 215 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 106 " 0.005 2.00e-02 2.50e+03 9.04e-03 8.17e-01 pdb=" C ARG A 106 " -0.016 2.00e-02 2.50e+03 pdb=" O ARG A 106 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL A 107 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 108 " -0.004 2.00e-02 2.50e+03 8.14e-03 6.63e-01 pdb=" C SER A 108 " 0.014 2.00e-02 2.50e+03 pdb=" O SER A 108 " -0.005 2.00e-02 2.50e+03 pdb=" N ARG A 109 " -0.005 2.00e-02 2.50e+03 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 391 2.73 - 3.27: 6781 3.27 - 3.82: 11622 3.82 - 4.36: 14987 4.36 - 4.90: 27656 Nonbonded interactions: 61437 Sorted by model distance: nonbonded pdb=" OG1 THR B 206 " pdb=" OD1 ASP B 214 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR B 213 " pdb=" O THR B 216 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR B 366 " pdb=" OG SER B 409 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 213 " pdb=" O THR A 216 " model vdw 2.264 3.040 nonbonded pdb=" O VAL A 105 " pdb=" OG SER A 108 " model vdw 2.279 3.040 ... (remaining 61432 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 17.710 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.090 Find NCS groups from input model: 0.110 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7521 Z= 0.127 Angle : 0.494 5.626 10140 Z= 0.292 Chirality : 0.043 0.168 1032 Planarity : 0.002 0.020 1362 Dihedral : 12.999 89.396 2682 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.28), residues: 957 helix: -0.57 (0.70), residues: 42 sheet: -0.41 (0.22), residues: 576 loop : -0.64 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.007 0.001 TYR B 187 PHE 0.013 0.001 PHE A 420 TRP 0.012 0.001 TRP B 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7521) covalent geometry : angle 0.49370 (10140) hydrogen bonds : bond 0.08640 ( 461) hydrogen bonds : angle 5.84857 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.228 Fit side-chains REVERT: A 275 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.6947 (mtm180) REVERT: A 304 LYS cc_start: 0.6869 (pptt) cc_final: 0.6392 (ptpp) REVERT: A 338 LYS cc_start: 0.8283 (tptp) cc_final: 0.7707 (mtmm) REVERT: B 139 ASN cc_start: 0.7843 (t0) cc_final: 0.7607 (t0) REVERT: B 184 ASP cc_start: 0.7969 (t0) cc_final: 0.7684 (t70) REVERT: C 118 LYS cc_start: 0.8581 (tttp) cc_final: 0.8311 (ttpp) REVERT: C 321 ASN cc_start: 0.7712 (m-40) cc_final: 0.7477 (m-40) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1150 time to fit residues: 17.6372 Evaluate side-chains 78 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 205 GLN A 221 GLN A 223 ASN A 232 GLN B 169 ASN B 370 ASN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115567 restraints weight = 8494.191| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.54 r_work: 0.3220 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7521 Z= 0.155 Angle : 0.493 4.902 10140 Z= 0.286 Chirality : 0.044 0.158 1032 Planarity : 0.002 0.019 1362 Dihedral : 4.179 15.574 1059 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.10 % Allowed : 4.72 % Favored : 93.18 % 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: -0.64 (0.28), residues: 957 helix: 2.50 (0.85), residues: 42 sheet: -0.36 (0.22), residues: 579 loop : -0.66 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.019 0.001 TYR A 187 PHE 0.014 0.001 PHE C 217 TRP 0.010 0.001 TRP B 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7521) covalent geometry : angle 0.49317 (10140) hydrogen bonds : bond 0.02951 ( 461) hydrogen bonds : angle 5.18505 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 187 TYR cc_start: 0.8999 (p90) cc_final: 0.8795 (p90) REVERT: A 304 LYS cc_start: 0.7094 (pptt) cc_final: 0.6328 (ptpp) REVERT: C 278 SER cc_start: 0.9002 (m) cc_final: 0.8758 (m) REVERT: C 321 ASN cc_start: 0.7891 (m-40) cc_final: 0.7585 (m-40) outliers start: 16 outliers final: 15 residues processed: 92 average time/residue: 0.1164 time to fit residues: 13.7515 Evaluate side-chains 88 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN C 221 GLN C 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115268 restraints weight = 8420.451| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.53 r_work: 0.3215 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7521 Z= 0.150 Angle : 0.475 4.916 10140 Z= 0.276 Chirality : 0.044 0.156 1032 Planarity : 0.002 0.019 1362 Dihedral : 4.170 15.065 1059 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.23 % Allowed : 6.17 % Favored : 91.60 % 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: -0.59 (0.28), residues: 957 helix: 2.87 (0.81), residues: 42 sheet: -0.35 (0.22), residues: 579 loop : -0.66 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.014 0.001 TYR A 187 PHE 0.012 0.001 PHE C 217 TRP 0.010 0.001 TRP C 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7521) covalent geometry : angle 0.47516 (10140) hydrogen bonds : bond 0.02828 ( 461) hydrogen bonds : angle 5.09797 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.257 Fit side-chains REVERT: A 187 TYR cc_start: 0.8996 (p90) cc_final: 0.8763 (p90) REVERT: A 338 LYS cc_start: 0.8350 (tptp) cc_final: 0.7557 (mtmm) REVERT: C 226 ASN cc_start: 0.8116 (t0) cc_final: 0.7871 (t0) REVERT: C 278 SER cc_start: 0.9027 (m) cc_final: 0.8792 (m) REVERT: C 321 ASN cc_start: 0.7909 (m-40) cc_final: 0.7596 (m-40) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.1103 time to fit residues: 13.1610 Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN B 370 ASN ** C 299 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111640 restraints weight = 8627.750| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.67 r_work: 0.3188 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7521 Z= 0.155 Angle : 0.472 4.887 10140 Z= 0.274 Chirality : 0.044 0.150 1032 Planarity : 0.002 0.019 1362 Dihedral : 4.172 14.917 1059 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.23 % Allowed : 7.61 % Favored : 90.16 % 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: -0.59 (0.28), residues: 957 helix: 3.24 (0.82), residues: 42 sheet: -0.36 (0.22), residues: 579 loop : -0.68 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 303 TYR 0.012 0.001 TYR A 187 PHE 0.013 0.001 PHE C 217 TRP 0.010 0.001 TRP C 325 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7521) covalent geometry : angle 0.47187 (10140) hydrogen bonds : bond 0.02766 ( 461) hydrogen bonds : angle 5.06272 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.242 Fit side-chains REVERT: A 180 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7576 (mm-40) REVERT: A 187 TYR cc_start: 0.9013 (p90) cc_final: 0.8730 (p90) REVERT: A 338 LYS cc_start: 0.8341 (tptp) cc_final: 0.7432 (mtmm) REVERT: C 226 ASN cc_start: 0.8107 (t0) cc_final: 0.7831 (t0) REVERT: C 278 SER cc_start: 0.9052 (m) cc_final: 0.8843 (m) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.0996 time to fit residues: 11.2175 Evaluate side-chains 87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111741 restraints weight = 8637.541| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.68 r_work: 0.3189 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7521 Z= 0.145 Angle : 0.463 4.782 10140 Z= 0.270 Chirality : 0.043 0.149 1032 Planarity : 0.002 0.017 1362 Dihedral : 4.139 14.982 1059 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.23 % Allowed : 9.32 % Favored : 88.45 % 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: -0.56 (0.28), residues: 957 helix: 3.45 (0.82), residues: 42 sheet: -0.35 (0.22), residues: 579 loop : -0.66 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 303 TYR 0.012 0.001 TYR C 331 PHE 0.012 0.001 PHE C 217 TRP 0.010 0.001 TRP C 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7521) covalent geometry : angle 0.46316 (10140) hydrogen bonds : bond 0.02701 ( 461) hydrogen bonds : angle 5.01007 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 187 TYR cc_start: 0.9020 (p90) cc_final: 0.8688 (p90) REVERT: C 226 ASN cc_start: 0.8048 (t0) cc_final: 0.7816 (t0) REVERT: C 278 SER cc_start: 0.9056 (m) cc_final: 0.8851 (m) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.1193 time to fit residues: 13.3071 Evaluate side-chains 87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 31 optimal weight: 0.6980 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108138 restraints weight = 8757.131| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.65 r_work: 0.3142 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 7521 Z= 0.290 Angle : 0.564 5.263 10140 Z= 0.322 Chirality : 0.046 0.159 1032 Planarity : 0.003 0.040 1362 Dihedral : 4.568 14.602 1059 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.49 % Allowed : 10.76 % Favored : 86.75 % 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: -0.93 (0.28), residues: 957 helix: 3.14 (0.83), residues: 42 sheet: -0.64 (0.22), residues: 594 loop : -0.78 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 303 TYR 0.015 0.002 TYR B 296 PHE 0.018 0.002 PHE C 217 TRP 0.011 0.002 TRP C 325 HIS 0.007 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 7521) covalent geometry : angle 0.56432 (10140) hydrogen bonds : bond 0.03230 ( 461) hydrogen bonds : angle 5.33298 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 240 ASP cc_start: 0.8403 (m-30) cc_final: 0.8102 (m-30) outliers start: 19 outliers final: 16 residues processed: 88 average time/residue: 0.1249 time to fit residues: 13.8482 Evaluate side-chains 85 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111023 restraints weight = 8635.695| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.66 r_work: 0.3178 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7521 Z= 0.133 Angle : 0.472 4.657 10140 Z= 0.276 Chirality : 0.043 0.149 1032 Planarity : 0.002 0.018 1362 Dihedral : 4.262 15.187 1059 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.23 % Allowed : 11.81 % Favored : 85.96 % 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: -0.69 (0.28), residues: 957 helix: 3.34 (0.84), residues: 42 sheet: -0.42 (0.22), residues: 579 loop : -0.77 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 303 TYR 0.011 0.001 TYR A 187 PHE 0.011 0.001 PHE C 217 TRP 0.011 0.001 TRP C 325 HIS 0.002 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7521) covalent geometry : angle 0.47156 (10140) hydrogen bonds : bond 0.02706 ( 461) hydrogen bonds : angle 5.07491 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.336 Fit side-chains REVERT: A 338 LYS cc_start: 0.8349 (tptp) cc_final: 0.7439 (mtmm) outliers start: 17 outliers final: 16 residues processed: 90 average time/residue: 0.1288 time to fit residues: 14.6605 Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 304 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111392 restraints weight = 8689.538| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.67 r_work: 0.3187 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7521 Z= 0.135 Angle : 0.465 4.604 10140 Z= 0.273 Chirality : 0.043 0.144 1032 Planarity : 0.002 0.016 1362 Dihedral : 4.153 14.556 1059 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.10 % Allowed : 12.34 % Favored : 85.56 % 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 (0.28), residues: 957 helix: 3.31 (0.84), residues: 42 sheet: -0.37 (0.22), residues: 579 loop : -0.72 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 303 TYR 0.014 0.001 TYR C 331 PHE 0.011 0.001 PHE C 217 TRP 0.010 0.001 TRP A 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7521) covalent geometry : angle 0.46454 (10140) hydrogen bonds : bond 0.02643 ( 461) hydrogen bonds : angle 4.97176 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: B 343 ASP cc_start: 0.8255 (t0) cc_final: 0.7956 (t70) outliers start: 16 outliers final: 15 residues processed: 87 average time/residue: 0.1246 time to fit residues: 13.7334 Evaluate side-chains 87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN C 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113767 restraints weight = 8494.069| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.54 r_work: 0.3190 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7521 Z= 0.165 Angle : 0.484 4.583 10140 Z= 0.283 Chirality : 0.044 0.144 1032 Planarity : 0.002 0.022 1362 Dihedral : 4.233 14.824 1059 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.49 % Allowed : 12.20 % Favored : 85.30 % 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: -0.66 (0.28), residues: 957 helix: 3.21 (0.82), residues: 42 sheet: -0.40 (0.22), residues: 579 loop : -0.75 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 303 TYR 0.011 0.001 TYR B 187 PHE 0.013 0.001 PHE C 217 TRP 0.010 0.001 TRP C 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7521) covalent geometry : angle 0.48378 (10140) hydrogen bonds : bond 0.02750 ( 461) hydrogen bonds : angle 5.01718 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.217 Fit side-chains REVERT: A 338 LYS cc_start: 0.8363 (tptp) cc_final: 0.7549 (mtmm) REVERT: B 343 ASP cc_start: 0.8232 (t0) cc_final: 0.7896 (t70) REVERT: C 278 SER cc_start: 0.9002 (m) cc_final: 0.8760 (m) outliers start: 19 outliers final: 19 residues processed: 88 average time/residue: 0.1203 time to fit residues: 13.5725 Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113575 restraints weight = 8492.907| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.60 r_work: 0.3190 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7521 Z= 0.154 Angle : 0.479 4.593 10140 Z= 0.280 Chirality : 0.044 0.144 1032 Planarity : 0.002 0.028 1362 Dihedral : 4.223 14.825 1059 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.62 % Allowed : 12.07 % Favored : 85.30 % 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: -0.66 (0.28), residues: 957 helix: 3.22 (0.82), residues: 42 sheet: -0.40 (0.22), residues: 579 loop : -0.74 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 303 TYR 0.014 0.001 TYR C 331 PHE 0.013 0.001 PHE C 217 TRP 0.010 0.001 TRP C 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7521) covalent geometry : angle 0.47918 (10140) hydrogen bonds : bond 0.02700 ( 461) hydrogen bonds : angle 5.00177 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.298 Fit side-chains REVERT: A 240 ASP cc_start: 0.8359 (m-30) cc_final: 0.8039 (m-30) REVERT: A 338 LYS cc_start: 0.8343 (tptp) cc_final: 0.7486 (mtmm) REVERT: B 343 ASP cc_start: 0.8255 (t0) cc_final: 0.7927 (t70) REVERT: C 278 SER cc_start: 0.9046 (m) cc_final: 0.8822 (m) outliers start: 20 outliers final: 19 residues processed: 88 average time/residue: 0.1250 time to fit residues: 14.0211 Evaluate side-chains 91 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN C 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110898 restraints weight = 8556.763| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.66 r_work: 0.3183 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7521 Z= 0.157 Angle : 0.485 6.174 10140 Z= 0.286 Chirality : 0.044 0.144 1032 Planarity : 0.002 0.028 1362 Dihedral : 4.224 14.825 1059 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.62 % Allowed : 12.47 % Favored : 84.91 % 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: -0.64 (0.28), residues: 957 helix: 3.29 (0.82), residues: 42 sheet: -0.39 (0.22), residues: 579 loop : -0.73 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 303 TYR 0.010 0.001 TYR A 187 PHE 0.013 0.001 PHE C 217 TRP 0.010 0.001 TRP C 325 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7521) covalent geometry : angle 0.48515 (10140) hydrogen bonds : bond 0.02695 ( 461) hydrogen bonds : angle 4.99892 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.43 seconds wall clock time: 37 minutes 17.06 seconds (2237.06 seconds total)