Starting phenix.real_space_refine on Thu Mar 5 03:33:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ng9_12310/03_2026/7ng9_12310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ng9_12310/03_2026/7ng9_12310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ng9_12310/03_2026/7ng9_12310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ng9_12310/03_2026/7ng9_12310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ng9_12310/03_2026/7ng9_12310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ng9_12310/03_2026/7ng9_12310.map" } resolution = 3.3 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 6021 2.51 5 N 1728 2.21 5 O 1995 1.98 5 H 9615 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19368 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6456 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 8, 'TRANS': 412} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, C Time building chain proxies: 5.76, per 1000 atoms: 0.30 Number of scatterers: 19368 At special positions: 0 Unit cell: (79.734, 82.2, 152.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 1995 8.00 N 1728 7.00 C 6021 6.00 H 9615 1.00 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: 1.56 Conformation dependent library (CDL) restraints added in 532.2 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 72.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.298A pdb=" N ASN A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 77 through 147 removed outlier: 3.564A pdb=" N TRP A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 187 removed outlier: 3.665A pdb=" N VAL A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 220 through 242 removed outlier: 3.571A pdb=" N LEU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 291 through 359 removed outlier: 4.056A pdb=" N LYS A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 398 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.534A pdb=" N LEU A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 14 through 36 removed outlier: 4.298A pdb=" N ASN B 32 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 77 through 147 removed outlier: 3.564A pdb=" N TRP B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 187 removed outlier: 3.664A pdb=" N VAL B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 Processing helix chain 'B' and resid 220 through 242 removed outlier: 3.570A pdb=" N LEU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 291 through 359 removed outlier: 4.055A pdb=" N LYS B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 398 Processing helix chain 'B' and resid 402 through 412 removed outlier: 3.535A pdb=" N LEU B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 36 removed outlier: 4.298A pdb=" N ASN C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 77 through 147 removed outlier: 3.564A pdb=" N TRP C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 187 removed outlier: 3.665A pdb=" N VAL C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 220 through 242 removed outlier: 3.570A pdb=" N LEU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 291 through 359 removed outlier: 4.055A pdb=" N LYS C 297 " --> pdb=" O ASN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 398 Processing helix chain 'C' and resid 402 through 412 removed outlier: 3.535A pdb=" N LEU C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 196 removed outlier: 4.825A pdb=" N LYS A 415 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.588A pdb=" N LYS A 277 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 48 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 258 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 4.021A pdb=" N TYR B 48 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 277 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 196 removed outlier: 4.825A pdb=" N LYS B 415 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 253 removed outlier: 3.588A pdb=" N LYS B 277 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 192 through 196 removed outlier: 4.825A pdb=" N LYS C 415 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 256 through 258 800 hydrogen bonds defined for protein. 2373 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: 4.87 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9615 1.03 - 1.22: 0 1.22 - 1.42: 4099 1.42 - 1.61: 5753 1.61 - 1.80: 18 Bond restraints: 19485 Sorted by residual: bond pdb=" N GLU C 1 " pdb=" H GLU C 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" N GLU A 1 " pdb=" H GLU A 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" N GLU B 1 " pdb=" H GLU B 1 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" N GLU B 1 " pdb=" CA GLU B 1 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.90e-02 2.77e+03 1.44e+00 bond pdb=" N GLU A 1 " pdb=" CA GLU A 1 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.90e-02 2.77e+03 1.37e+00 ... (remaining 19480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 33842 1.17 - 2.35: 1112 2.35 - 3.52: 62 3.52 - 4.69: 15 4.69 - 5.87: 6 Bond angle restraints: 35037 Sorted by residual: angle pdb=" C ARG B 55 " pdb=" N ASP B 56 " pdb=" CA ASP B 56 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.43e+00 angle pdb=" C ARG A 55 " pdb=" N ASP A 56 " pdb=" CA ASP A 56 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.35e+00 angle pdb=" C ARG C 55 " pdb=" N ASP C 56 " pdb=" CA ASP C 56 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.12e+00 angle pdb=" N SER C 36 " pdb=" CA SER C 36 " pdb=" C SER C 36 " ideal model delta sigma weight residual 109.81 113.55 -3.74 2.21e+00 2.05e-01 2.86e+00 angle pdb=" N SER B 36 " pdb=" CA SER B 36 " pdb=" C SER B 36 " ideal model delta sigma weight residual 109.81 113.54 -3.73 2.21e+00 2.05e-01 2.85e+00 ... (remaining 35032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8382 17.77 - 35.54: 585 35.54 - 53.31: 171 53.31 - 71.08: 33 71.08 - 88.86: 18 Dihedral angle restraints: 9189 sinusoidal: 5067 harmonic: 4122 Sorted by residual: dihedral pdb=" CA ASP B 77 " pdb=" CB ASP B 77 " pdb=" CG ASP B 77 " pdb=" OD1 ASP B 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.17 58.17 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP C 77 " pdb=" CB ASP C 77 " pdb=" CG ASP C 77 " pdb=" OD1 ASP C 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.12 58.12 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.11 58.11 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 891 0.025 - 0.050: 420 0.050 - 0.075: 174 0.075 - 0.099: 66 0.099 - 0.124: 15 Chirality restraints: 1566 Sorted by residual: chirality pdb=" CA PRO B 37 " pdb=" N PRO B 37 " pdb=" C PRO B 37 " pdb=" CB PRO B 37 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA PRO A 15 " pdb=" N PRO A 15 " pdb=" C PRO A 15 " pdb=" CB PRO A 15 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA PRO C 15 " pdb=" N PRO C 15 " pdb=" C PRO C 15 " pdb=" CB PRO C 15 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1563 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 14 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO C 15 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 15 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 15 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 14 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO A 15 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 14 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 15 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " 0.015 5.00e-02 4.00e+02 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1250 2.20 - 2.80: 41932 2.80 - 3.40: 52821 3.40 - 4.00: 68081 4.00 - 4.60: 110656 Nonbonded interactions: 274740 Sorted by model distance: nonbonded pdb="HE22 GLN A 298 " pdb=" OE1 GLU C 33 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU B 33 " pdb="HE22 GLN C 298 " model vdw 1.617 2.450 nonbonded pdb=" OD1 ASN A 2 " pdb=" H LEU A 3 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASN C 2 " pdb=" H LEU C 3 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASN B 2 " pdb=" H LEU B 3 " model vdw 1.640 2.450 ... (remaining 274735 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: 0.03 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: 0.850 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: 0.100 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.041 9870 Z= 0.269 Angle : 0.480 5.867 13401 Z= 0.276 Chirality : 0.036 0.124 1566 Planarity : 0.003 0.028 1785 Dihedral : 14.724 88.855 3636 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.85 % Allowed : 9.89 % Favored : 89.27 % 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: -0.87 (0.22), residues: 1257 helix: 1.19 (0.16), residues: 780 sheet: -4.18 (0.27), residues: 204 loop : -2.63 (0.29), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 183 TYR 0.009 0.001 TYR B 374 PHE 0.008 0.001 PHE A 325 TRP 0.003 0.001 TRP C 81 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 9870) covalent geometry : angle 0.48040 (13401) hydrogen bonds : bond 0.08970 ( 800) hydrogen bonds : angle 4.78420 ( 2373) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.6068 (OUTLIER) cc_final: 0.5734 (t70) REVERT: C 261 TYR cc_start: 0.8661 (m-80) cc_final: 0.8260 (m-80) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.1537 time to fit residues: 15.6702 Evaluate side-chains 53 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 317 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN B 41 GLN B 188 ASN B 230 GLN C 188 ASN C 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117058 restraints weight = 27824.932| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.83 r_work: 0.3127 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9870 Z= 0.162 Angle : 0.470 4.296 13401 Z= 0.263 Chirality : 0.034 0.122 1566 Planarity : 0.003 0.023 1785 Dihedral : 4.364 46.963 1389 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.41 % Allowed : 10.55 % Favored : 88.04 % 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: 1.39 (0.25), residues: 1257 helix: 3.07 (0.16), residues: 816 sheet: -4.12 (0.25), residues: 222 loop : -1.86 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.012 0.001 TYR A 374 PHE 0.009 0.001 PHE A 28 TRP 0.004 0.001 TRP C 81 HIS 0.008 0.002 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9870) covalent geometry : angle 0.46992 (13401) hydrogen bonds : bond 0.05827 ( 800) hydrogen bonds : angle 3.83420 ( 2373) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.455 Fit side-chains REVERT: B 12 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7834 (mt) REVERT: B 174 ASP cc_start: 0.7915 (m-30) cc_final: 0.7670 (m-30) REVERT: C 261 TYR cc_start: 0.8693 (m-80) cc_final: 0.8275 (m-80) REVERT: C 352 MET cc_start: 0.8094 (mtt) cc_final: 0.7675 (mtt) outliers start: 15 outliers final: 4 residues processed: 73 average time/residue: 0.1635 time to fit residues: 17.9175 Evaluate side-chains 57 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 249 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 188 ASN B 14 ASN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.132660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111826 restraints weight = 28861.102| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 0.84 r_work: 0.3081 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9870 Z= 0.176 Angle : 0.454 4.522 13401 Z= 0.254 Chirality : 0.034 0.119 1566 Planarity : 0.003 0.023 1785 Dihedral : 4.338 51.200 1383 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.85 % Allowed : 11.77 % Favored : 87.38 % 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: 1.69 (0.25), residues: 1257 helix: 3.27 (0.16), residues: 816 sheet: -4.02 (0.25), residues: 222 loop : -1.62 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 172 TYR 0.013 0.001 TYR A 374 PHE 0.013 0.001 PHE C 282 TRP 0.004 0.001 TRP C 81 HIS 0.006 0.002 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9870) covalent geometry : angle 0.45389 (13401) hydrogen bonds : bond 0.06035 ( 800) hydrogen bonds : angle 3.81261 ( 2373) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.457 Fit side-chains REVERT: A 202 LYS cc_start: 0.7588 (ptmm) cc_final: 0.7192 (ptpt) REVERT: A 350 ASP cc_start: 0.7859 (t70) cc_final: 0.7640 (t0) REVERT: B 174 ASP cc_start: 0.7801 (m-30) cc_final: 0.7497 (m-30) REVERT: B 202 LYS cc_start: 0.7775 (ptmm) cc_final: 0.7452 (ptpt) REVERT: C 202 LYS cc_start: 0.7704 (ptmm) cc_final: 0.7446 (ptpt) REVERT: C 261 TYR cc_start: 0.8801 (m-80) cc_final: 0.8379 (m-80) REVERT: C 352 MET cc_start: 0.8205 (mtt) cc_final: 0.7899 (mtt) outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 0.1995 time to fit residues: 24.2546 Evaluate side-chains 69 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 249 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 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 = 0.3456 r_free = 0.3456 target = 0.136340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114664 restraints weight = 28396.787| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 0.81 r_work: 0.3096 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9870 Z= 0.115 Angle : 0.395 3.894 13401 Z= 0.222 Chirality : 0.032 0.118 1566 Planarity : 0.003 0.025 1785 Dihedral : 4.149 50.585 1383 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.13 % Allowed : 11.96 % Favored : 86.91 % 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: 2.23 (0.25), residues: 1257 helix: 3.68 (0.16), residues: 816 sheet: -3.68 (0.28), residues: 216 loop : -1.65 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 227 TYR 0.011 0.001 TYR A 134 PHE 0.009 0.001 PHE C 325 TRP 0.001 0.000 TRP C 81 HIS 0.005 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9870) covalent geometry : angle 0.39518 (13401) hydrogen bonds : bond 0.05301 ( 800) hydrogen bonds : angle 3.52769 ( 2373) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.360 Fit side-chains REVERT: A 202 LYS cc_start: 0.7534 (ptmm) cc_final: 0.7143 (ptpt) REVERT: B 174 ASP cc_start: 0.7899 (m-30) cc_final: 0.7511 (m-30) REVERT: B 202 LYS cc_start: 0.7695 (ptmm) cc_final: 0.7407 (ptpt) REVERT: B 273 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7729 (pt) REVERT: C 202 LYS cc_start: 0.7664 (ptmm) cc_final: 0.7398 (ptpt) REVERT: C 217 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7237 (mm-30) REVERT: C 261 TYR cc_start: 0.8702 (m-80) cc_final: 0.8265 (m-80) REVERT: C 272 ASP cc_start: 0.5960 (p0) cc_final: 0.5471 (p0) REVERT: C 350 ASP cc_start: 0.8054 (t70) cc_final: 0.7762 (t0) REVERT: C 352 MET cc_start: 0.8287 (mtt) cc_final: 0.7912 (mtt) outliers start: 12 outliers final: 9 residues processed: 81 average time/residue: 0.2030 time to fit residues: 23.2982 Evaluate side-chains 70 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 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 = 0.3453 r_free = 0.3453 target = 0.136086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114727 restraints weight = 28310.477| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 0.84 r_work: 0.3087 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9870 Z= 0.116 Angle : 0.392 3.901 13401 Z= 0.220 Chirality : 0.032 0.117 1566 Planarity : 0.002 0.025 1785 Dihedral : 4.114 51.084 1383 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.85 % Allowed : 12.24 % Favored : 86.91 % 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: 2.43 (0.25), residues: 1257 helix: 3.81 (0.16), residues: 816 sheet: -3.56 (0.28), residues: 216 loop : -1.57 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 82 TYR 0.011 0.001 TYR C 134 PHE 0.008 0.001 PHE A 325 TRP 0.001 0.000 TRP A 81 HIS 0.004 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9870) covalent geometry : angle 0.39154 (13401) hydrogen bonds : bond 0.05218 ( 800) hydrogen bonds : angle 3.46387 ( 2373) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.458 Fit side-chains REVERT: A 202 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7245 (ptpt) REVERT: B 174 ASP cc_start: 0.7940 (m-30) cc_final: 0.7569 (m-30) REVERT: B 202 LYS cc_start: 0.7711 (ptmm) cc_final: 0.7338 (ptpt) REVERT: B 273 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7778 (pt) REVERT: C 202 LYS cc_start: 0.7730 (ptmm) cc_final: 0.7440 (ptpt) REVERT: C 261 TYR cc_start: 0.8684 (m-80) cc_final: 0.8248 (m-80) REVERT: C 272 ASP cc_start: 0.6101 (p0) cc_final: 0.5615 (p0) REVERT: C 350 ASP cc_start: 0.8090 (t70) cc_final: 0.7809 (t0) REVERT: C 352 MET cc_start: 0.8279 (mtt) cc_final: 0.7893 (mtt) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.1829 time to fit residues: 20.0412 Evaluate side-chains 67 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 249 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.134789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113186 restraints weight = 28525.318| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 0.78 r_work: 0.3076 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9870 Z= 0.131 Angle : 0.404 4.053 13401 Z= 0.227 Chirality : 0.032 0.117 1566 Planarity : 0.003 0.026 1785 Dihedral : 4.134 50.761 1383 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.69 % Allowed : 11.86 % Favored : 86.44 % 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: 2.43 (0.25), residues: 1257 helix: 3.78 (0.16), residues: 816 sheet: -3.49 (0.29), residues: 216 loop : -1.49 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 82 TYR 0.011 0.001 TYR B 374 PHE 0.008 0.001 PHE A 325 TRP 0.001 0.000 TRP C 81 HIS 0.004 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9870) covalent geometry : angle 0.40359 (13401) hydrogen bonds : bond 0.05358 ( 800) hydrogen bonds : angle 3.50044 ( 2373) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.460 Fit side-chains REVERT: A 202 LYS cc_start: 0.7597 (ptmm) cc_final: 0.7246 (ptpt) REVERT: A 272 ASP cc_start: 0.6263 (p0) cc_final: 0.5814 (p0) REVERT: B 174 ASP cc_start: 0.7875 (m-30) cc_final: 0.7495 (m-30) REVERT: B 202 LYS cc_start: 0.7737 (ptmm) cc_final: 0.7371 (ptpt) REVERT: B 272 ASP cc_start: 0.6376 (p0) cc_final: 0.5856 (p0) REVERT: B 273 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7828 (pt) REVERT: C 202 LYS cc_start: 0.7838 (ptmm) cc_final: 0.7544 (ptpt) REVERT: C 217 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7218 (mm-30) REVERT: C 261 TYR cc_start: 0.8699 (m-80) cc_final: 0.8260 (m-80) REVERT: C 272 ASP cc_start: 0.6233 (p0) cc_final: 0.5740 (p0) REVERT: C 350 ASP cc_start: 0.8100 (t70) cc_final: 0.7807 (t0) REVERT: C 352 MET cc_start: 0.8281 (mtt) cc_final: 0.7891 (mtt) outliers start: 18 outliers final: 14 residues processed: 102 average time/residue: 0.1765 time to fit residues: 26.7894 Evaluate side-chains 93 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114408 restraints weight = 28703.382| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 0.79 r_work: 0.3082 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9870 Z= 0.122 Angle : 0.399 3.939 13401 Z= 0.225 Chirality : 0.032 0.116 1566 Planarity : 0.003 0.026 1785 Dihedral : 4.108 50.927 1383 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.69 % Allowed : 11.68 % Favored : 86.63 % 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: 2.49 (0.25), residues: 1257 helix: 3.82 (0.16), residues: 816 sheet: -3.44 (0.29), residues: 216 loop : -1.47 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 18 TYR 0.014 0.001 TYR A 287 PHE 0.008 0.001 PHE A 325 TRP 0.001 0.000 TRP C 81 HIS 0.003 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9870) covalent geometry : angle 0.39938 (13401) hydrogen bonds : bond 0.05260 ( 800) hydrogen bonds : angle 3.47459 ( 2373) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7667 (ptmm) cc_final: 0.7304 (ptpt) REVERT: A 272 ASP cc_start: 0.6284 (p0) cc_final: 0.5838 (p0) REVERT: B 174 ASP cc_start: 0.7677 (m-30) cc_final: 0.7291 (m-30) REVERT: B 202 LYS cc_start: 0.7759 (ptmm) cc_final: 0.7417 (ptpt) REVERT: B 272 ASP cc_start: 0.6408 (p0) cc_final: 0.5879 (p0) REVERT: B 273 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7792 (pt) REVERT: C 202 LYS cc_start: 0.7827 (ptmm) cc_final: 0.7557 (ptpt) REVERT: C 261 TYR cc_start: 0.8713 (m-80) cc_final: 0.8287 (m-80) REVERT: C 272 ASP cc_start: 0.6221 (p0) cc_final: 0.5740 (p0) REVERT: C 350 ASP cc_start: 0.7940 (t70) cc_final: 0.7684 (t0) outliers start: 18 outliers final: 13 residues processed: 103 average time/residue: 0.1786 time to fit residues: 27.4108 Evaluate side-chains 93 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 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 = 0.3446 r_free = 0.3446 target = 0.135566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114200 restraints weight = 28656.476| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 0.76 r_work: 0.3092 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9870 Z= 0.120 Angle : 0.397 4.091 13401 Z= 0.222 Chirality : 0.032 0.117 1566 Planarity : 0.003 0.025 1785 Dihedral : 4.096 51.204 1383 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.32 % Allowed : 12.34 % Favored : 86.35 % 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: 2.53 (0.25), residues: 1257 helix: 3.84 (0.16), residues: 816 sheet: -3.41 (0.29), residues: 216 loop : -1.41 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 82 TYR 0.022 0.001 TYR B 287 PHE 0.008 0.001 PHE A 325 TRP 0.001 0.000 TRP A 81 HIS 0.005 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9870) covalent geometry : angle 0.39676 (13401) hydrogen bonds : bond 0.05195 ( 800) hydrogen bonds : angle 3.44441 ( 2373) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7652 (ptmm) cc_final: 0.7290 (ptpt) REVERT: A 272 ASP cc_start: 0.6367 (p0) cc_final: 0.5907 (p0) REVERT: B 174 ASP cc_start: 0.7852 (m-30) cc_final: 0.7485 (m-30) REVERT: B 202 LYS cc_start: 0.7755 (ptmm) cc_final: 0.7409 (ptpt) REVERT: B 272 ASP cc_start: 0.6495 (p0) cc_final: 0.5967 (p0) REVERT: B 273 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7881 (pt) REVERT: C 202 LYS cc_start: 0.7805 (ptmm) cc_final: 0.7518 (ptpt) REVERT: C 261 TYR cc_start: 0.8707 (m-80) cc_final: 0.8273 (m-80) REVERT: C 272 ASP cc_start: 0.6296 (p0) cc_final: 0.5854 (p0) REVERT: C 350 ASP cc_start: 0.8062 (t70) cc_final: 0.7774 (t0) REVERT: C 352 MET cc_start: 0.8271 (mtt) cc_final: 0.7746 (mtt) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.1853 time to fit residues: 26.1510 Evaluate side-chains 92 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 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 = 0.3428 r_free = 0.3428 target = 0.134163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112829 restraints weight = 28754.627| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.76 r_work: 0.3039 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9870 Z= 0.133 Angle : 0.409 4.136 13401 Z= 0.229 Chirality : 0.032 0.116 1566 Planarity : 0.003 0.025 1785 Dihedral : 4.151 51.969 1383 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.13 % Allowed : 12.52 % Favored : 86.35 % 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: 2.47 (0.25), residues: 1257 helix: 3.77 (0.16), residues: 816 sheet: -3.38 (0.29), residues: 216 loop : -1.41 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 82 TYR 0.014 0.001 TYR B 287 PHE 0.008 0.001 PHE A 325 TRP 0.001 0.000 TRP C 81 HIS 0.006 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9870) covalent geometry : angle 0.40908 (13401) hydrogen bonds : bond 0.05352 ( 800) hydrogen bonds : angle 3.49640 ( 2373) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7643 (ptmm) cc_final: 0.7313 (ptpt) REVERT: A 272 ASP cc_start: 0.6426 (p0) cc_final: 0.5999 (p0) REVERT: B 174 ASP cc_start: 0.7904 (m-30) cc_final: 0.7526 (m-30) REVERT: B 202 LYS cc_start: 0.7749 (ptmm) cc_final: 0.7402 (ptpt) REVERT: B 272 ASP cc_start: 0.6585 (p0) cc_final: 0.6084 (p0) REVERT: B 273 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7953 (pt) REVERT: C 202 LYS cc_start: 0.7807 (ptmm) cc_final: 0.7538 (ptpt) REVERT: C 261 TYR cc_start: 0.8701 (m-80) cc_final: 0.8160 (m-80) REVERT: C 272 ASP cc_start: 0.6437 (p0) cc_final: 0.5985 (p0) REVERT: C 350 ASP cc_start: 0.8070 (t70) cc_final: 0.7805 (t0) REVERT: C 352 MET cc_start: 0.8316 (mtt) cc_final: 0.7797 (mtt) outliers start: 12 outliers final: 11 residues processed: 108 average time/residue: 0.1737 time to fit residues: 27.9330 Evaluate side-chains 101 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 85 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114404 restraints weight = 28648.152| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 0.76 r_work: 0.3123 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9870 Z= 0.115 Angle : 0.400 4.362 13401 Z= 0.224 Chirality : 0.032 0.117 1566 Planarity : 0.002 0.025 1785 Dihedral : 4.093 51.643 1383 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.32 % Allowed : 12.62 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.25), residues: 1257 helix: 3.86 (0.16), residues: 816 sheet: -3.33 (0.30), residues: 216 loop : -1.39 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 82 TYR 0.013 0.001 TYR B 287 PHE 0.009 0.001 PHE C 325 TRP 0.002 0.000 TRP C 81 HIS 0.005 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9870) covalent geometry : angle 0.40015 (13401) hydrogen bonds : bond 0.05166 ( 800) hydrogen bonds : angle 3.44614 ( 2373) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Residue LYS 415 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7661 (ptmm) cc_final: 0.7320 (ptpt) REVERT: A 272 ASP cc_start: 0.6419 (p0) cc_final: 0.6000 (p0) REVERT: B 174 ASP cc_start: 0.7662 (m-30) cc_final: 0.7269 (m-30) REVERT: B 202 LYS cc_start: 0.7778 (ptmm) cc_final: 0.7441 (ptpt) REVERT: B 272 ASP cc_start: 0.6596 (p0) cc_final: 0.6054 (p0) REVERT: B 273 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7859 (pt) REVERT: C 191 PRO cc_start: 0.8592 (Cg_endo) cc_final: 0.8362 (Cg_exo) REVERT: C 202 LYS cc_start: 0.7798 (ptmm) cc_final: 0.7543 (ptpt) REVERT: C 261 TYR cc_start: 0.8651 (m-80) cc_final: 0.8250 (m-80) REVERT: C 272 ASP cc_start: 0.6388 (p0) cc_final: 0.5914 (p0) REVERT: C 350 ASP cc_start: 0.7993 (t70) cc_final: 0.7716 (t0) REVERT: C 352 MET cc_start: 0.8205 (mtt) cc_final: 0.7695 (mtt) outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.1915 time to fit residues: 25.6232 Evaluate side-chains 89 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 420 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.109228 restraints weight = 29118.614| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 0.76 r_work: 0.3026 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9870 Z= 0.185 Angle : 0.464 4.466 13401 Z= 0.260 Chirality : 0.035 0.127 1566 Planarity : 0.003 0.025 1785 Dihedral : 4.371 53.598 1383 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.41 % Allowed : 12.71 % Favored : 85.88 % 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: 2.19 (0.25), residues: 1257 helix: 3.51 (0.16), residues: 816 sheet: -3.41 (0.30), residues: 216 loop : -1.40 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 322 TYR 0.014 0.002 TYR B 287 PHE 0.009 0.001 PHE C 325 TRP 0.002 0.001 TRP C 81 HIS 0.007 0.002 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9870) covalent geometry : angle 0.46382 (13401) hydrogen bonds : bond 0.05970 ( 800) hydrogen bonds : angle 3.70302 ( 2373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3702.82 seconds wall clock time: 64 minutes 26.34 seconds (3866.34 seconds total)