Starting phenix.real_space_refine on Thu Jul 2 11:19:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmr_48401/07_2026/9mmr_48401.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmr_48401/07_2026/9mmr_48401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmr_48401/07_2026/9mmr_48401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmr_48401/07_2026/9mmr_48401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmr_48401/07_2026/9mmr_48401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmr_48401/07_2026/9mmr_48401.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians I 1 10.91 5 P 7 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5167 2.51 5 N 1391 2.21 5 O 1566 1.98 5 F 1 1.80 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8182 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2236 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 270} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2178 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain breaks: 1 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.92, per 1000 atoms: 0.23 Number of scatterers: 8182 At special positions: 0 Unit cell: (78.11, 94.9, 111.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 1 52.95 S 47 16.00 P 7 15.00 Mg 2 11.99 F 1 9.00 O 1566 8.00 N 1391 7.00 C 5167 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: 0.72 Conformation dependent library (CDL) restraints added in 471.4 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 63.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 441 through 462 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.609A pdb=" N SER A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 526 through 544 removed outlier: 3.539A pdb=" N ASP A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.651A pdb=" N LYS A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.618A pdb=" N VAL A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 162 through 184 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 242 through 258 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.521A pdb=" N VAL B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 37 through 70 removed outlier: 3.730A pdb=" N ASN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 102 removed outlier: 4.110A pdb=" N GLN C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 133 removed outlier: 3.968A pdb=" N VAL C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 160 removed outlier: 3.528A pdb=" N VAL C 141 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 181 Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.841A pdb=" N GLU C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 230 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.864A pdb=" N THR D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY D 33 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 67 removed outlier: 3.623A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 104 removed outlier: 4.091A pdb=" N GLU D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 133 removed outlier: 3.747A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 160 removed outlier: 3.543A pdb=" N ASN D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 181 Processing helix chain 'D' and resid 184 through 202 Processing helix chain 'D' and resid 212 through 230 removed outlier: 3.645A pdb=" N SER D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 357 removed outlier: 4.198A pdb=" N LYS A 365 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ARG A 354 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL A 363 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY A 356 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLY A 361 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 497 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 76 removed outlier: 6.769A pdb=" N LYS B 84 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU B 73 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 82 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLY B 75 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLY B 80 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 92 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.765A pdb=" N GLY B 149 " --> pdb=" O VAL B 198 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1500 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: 1.27 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3253 1.39 - 1.55: 4984 1.55 - 1.71: 18 1.71 - 1.87: 78 1.87 - 2.03: 3 Bond restraints: 8336 Sorted by residual: bond pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " ideal model delta sigma weight residual 1.673 1.569 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O3B AGS B 701 " pdb=" PB AGS B 701 " ideal model delta sigma weight residual 1.673 1.573 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O3A AGS A 701 " pdb=" PA AGS A 701 " ideal model delta sigma weight residual 1.664 1.571 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3A AGS B 701 " pdb=" PA AGS B 701 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C23 LCJ B 703 " pdb=" I01 LCJ B 703 " ideal model delta sigma weight residual 2.099 2.027 0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 8331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 11100 2.45 - 4.89: 135 4.89 - 7.34: 18 7.34 - 9.79: 7 9.79 - 12.23: 3 Bond angle restraints: 11263 Sorted by residual: angle pdb=" N PRO B 264 " pdb=" CA PRO B 264 " pdb=" C PRO B 264 " ideal model delta sigma weight residual 110.70 98.74 11.96 1.22e+00 6.72e-01 9.61e+01 angle pdb=" PB AGS B 701 " pdb=" O3B AGS B 701 " pdb=" PG AGS B 701 " ideal model delta sigma weight residual 129.21 116.98 12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA HIS B 188 " pdb=" C HIS B 188 " pdb=" O HIS B 188 " ideal model delta sigma weight residual 120.82 116.86 3.96 1.05e+00 9.07e-01 1.42e+01 angle pdb=" PB AGS A 701 " pdb=" O3B AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sigma weight residual 129.21 118.35 10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C ILE B 196 " pdb=" CA ILE B 196 " pdb=" CB ILE B 196 " ideal model delta sigma weight residual 110.83 115.64 -4.81 1.49e+00 4.50e-01 1.04e+01 ... (remaining 11258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 5016 28.79 - 57.57: 101 57.57 - 86.36: 16 86.36 - 115.15: 3 115.15 - 143.93: 6 Dihedral angle restraints: 5142 sinusoidal: 2153 harmonic: 2989 Sorted by residual: dihedral pdb=" CD ARG C 222 " pdb=" NE ARG C 222 " pdb=" CZ ARG C 222 " pdb=" NH1 ARG C 222 " ideal model delta sinusoidal sigma weight residual 0.00 -39.89 39.89 1 1.00e+01 1.00e-02 2.23e+01 dihedral pdb=" O3A AGS A 701 " pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sinusoidal sigma weight residual -107.39 36.54 -143.93 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" O2B AGS A 701 " pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sinusoidal sigma weight residual 7.37 149.73 -142.36 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1027 0.052 - 0.104: 183 0.104 - 0.156: 28 0.156 - 0.208: 2 0.208 - 0.260: 2 Chirality restraints: 1242 Sorted by residual: chirality pdb=" C3' AGS A 701 " pdb=" C2' AGS A 701 " pdb=" C4' AGS A 701 " pdb=" O3' AGS A 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' AGS B 701 " pdb=" C2' AGS B 701 " pdb=" C4' AGS B 701 " pdb=" O3' AGS B 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.60 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE B 196 " pdb=" CA ILE B 196 " pdb=" CG1 ILE B 196 " pdb=" CG2 ILE B 196 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 1239 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 222 " -0.701 9.50e-02 1.11e+02 3.14e-01 6.03e+01 pdb=" NE ARG C 222 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG C 222 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 222 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 222 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 383 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 384 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 599 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 600 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " 0.023 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 40 2.40 - 3.04: 5510 3.04 - 3.68: 13138 3.68 - 4.32: 19705 4.32 - 4.96: 33127 Nonbonded interactions: 71520 Sorted by model distance: nonbonded pdb=" O2A AGS A 701 " pdb="MG MG A 702 " model vdw 1.765 2.170 nonbonded pdb=" O3A AGS B 701 " pdb="MG MG B 702 " model vdw 1.799 2.170 nonbonded pdb=" OD2 ASP A 486 " pdb="MG MG A 702 " model vdw 1.876 2.170 nonbonded pdb=" O1B AGS A 701 " pdb="MG MG A 702 " model vdw 1.974 2.170 nonbonded pdb=" PB AGS B 701 " pdb="MG MG B 702 " model vdw 2.054 2.530 ... (remaining 71515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) selection = chain 'D' } 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 group one per residue 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: 3.800 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.860 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.005 0.104 8336 Z= 0.296 Angle : 0.734 12.232 11263 Z= 0.407 Chirality : 0.041 0.260 1242 Planarity : 0.009 0.314 1435 Dihedral : 13.567 143.933 3210 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.57 % Allowed : 6.58 % Favored : 92.85 % 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: 1.15 (0.26), residues: 1007 helix: 1.78 (0.21), residues: 601 sheet: -0.68 (0.63), residues: 50 loop : -0.78 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 83 TYR 0.020 0.002 TYR D 128 PHE 0.018 0.002 PHE C 117 TRP 0.014 0.001 TRP D 59 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.30 ( 8336) covalent geometry : angle 0.73383 / 0.41 (11263) hydrogen bonds : bond 0.13424 / 8.75 ( 507) hydrogen bonds : angle 5.56415 / 4.11 ( 1500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8161 (mttm) cc_final: 0.7810 (pttm) REVERT: A 401 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7938 (tpp80) REVERT: A 412 MET cc_start: 0.6915 (ptp) cc_final: 0.6688 (ptm) REVERT: A 469 MET cc_start: 0.8679 (tpt) cc_final: 0.8368 (tpt) REVERT: B 94 MET cc_start: 0.7793 (ptp) cc_final: 0.7560 (ptm) REVERT: B 142 CYS cc_start: 0.8902 (m) cc_final: 0.7434 (m) REVERT: B 143 MET cc_start: 0.8005 (ptt) cc_final: 0.7092 (ptp) REVERT: B 184 HIS cc_start: 0.8214 (m-70) cc_final: 0.6888 (m90) REVERT: B 236 GLN cc_start: 0.8709 (mt0) cc_final: 0.8429 (mm-40) REVERT: B 356 MET cc_start: 0.7912 (mtp) cc_final: 0.7607 (mtp) REVERT: C 19 TYR cc_start: 0.7421 (m-80) cc_final: 0.6949 (m-10) REVERT: C 59 TRP cc_start: 0.8876 (t60) cc_final: 0.8260 (t60) REVERT: C 93 ILE cc_start: 0.9212 (mt) cc_final: 0.8996 (mt) REVERT: C 215 THR cc_start: 0.9156 (t) cc_final: 0.8722 (p) REVERT: C 223 ASP cc_start: 0.9527 (m-30) cc_final: 0.9166 (m-30) REVERT: D 14 GLU cc_start: 0.8885 (tt0) cc_final: 0.8638 (tp30) REVERT: D 17 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8164 (tm-30) REVERT: D 116 VAL cc_start: 0.9422 (t) cc_final: 0.9209 (t) REVERT: D 139 ASN cc_start: 0.9453 (m-40) cc_final: 0.9140 (m-40) REVERT: D 146 GLN cc_start: 0.9242 (mt0) cc_final: 0.8956 (mt0) REVERT: D 155 ILE cc_start: 0.9515 (mt) cc_final: 0.9178 (tp) REVERT: D 194 GLN cc_start: 0.9171 (mt0) cc_final: 0.8959 (pt0) outliers start: 5 outliers final: 4 residues processed: 322 average time/residue: 0.1152 time to fit residues: 47.6930 Evaluate side-chains 194 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 610 GLN B 145 HIS B 153 GLN B 345 ASN C 42 ASN C 50 ASN D 173 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.073381 restraints weight = 33661.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.075148 restraints weight = 21930.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.076407 restraints weight = 16222.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.077321 restraints weight = 12947.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.078029 restraints weight = 10959.100| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8336 Z= 0.152 Angle : 0.681 9.341 11263 Z= 0.350 Chirality : 0.042 0.157 1242 Planarity : 0.004 0.050 1435 Dihedral : 13.725 126.489 1204 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.61 % Allowed : 16.91 % Favored : 80.48 % 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: 1.16 (0.26), residues: 1007 helix: 1.77 (0.20), residues: 614 sheet: -0.45 (0.57), residues: 58 loop : -0.88 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 450 TYR 0.016 0.002 TYR D 128 PHE 0.015 0.002 PHE D 196 TRP 0.013 0.001 TRP D 59 HIS 0.006 0.001 HIS D 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 8336) covalent geometry : angle 0.68133 / 0.35 (11263) hydrogen bonds : bond 0.04741 / 3.11 ( 507) hydrogen bonds : angle 4.64042 / 3.38 ( 1500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8287 (mttm) cc_final: 0.7918 (pttm) REVERT: A 401 ARG cc_start: 0.7956 (tpp-160) cc_final: 0.7589 (tpp80) REVERT: A 412 MET cc_start: 0.7076 (ptp) cc_final: 0.6854 (ptm) REVERT: A 456 MET cc_start: 0.8626 (mmm) cc_final: 0.8214 (mmm) REVERT: A 622 GLU cc_start: 0.8486 (tp30) cc_final: 0.8269 (tp30) REVERT: B 94 MET cc_start: 0.7489 (ptp) cc_final: 0.7241 (ptm) REVERT: B 142 CYS cc_start: 0.8391 (m) cc_final: 0.7085 (m) REVERT: B 143 MET cc_start: 0.8115 (ptt) cc_final: 0.7569 (ptp) REVERT: B 185 LYS cc_start: 0.8437 (tptt) cc_final: 0.7995 (tppt) REVERT: C 8 GLN cc_start: 0.9008 (pp30) cc_final: 0.8756 (pp30) REVERT: C 26 MET cc_start: 0.9107 (mmm) cc_final: 0.8355 (mmm) REVERT: C 59 TRP cc_start: 0.8551 (t60) cc_final: 0.8216 (t60) REVERT: C 198 ASP cc_start: 0.8809 (t0) cc_final: 0.8602 (t0) REVERT: C 215 THR cc_start: 0.8605 (t) cc_final: 0.8402 (p) REVERT: D 14 GLU cc_start: 0.8724 (tt0) cc_final: 0.8413 (tp30) REVERT: D 17 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7862 (tm-30) REVERT: D 22 MET cc_start: 0.7535 (ptm) cc_final: 0.7264 (ptm) REVERT: D 139 ASN cc_start: 0.9363 (m-40) cc_final: 0.9033 (m-40) REVERT: D 146 GLN cc_start: 0.8893 (mt0) cc_final: 0.8688 (mt0) REVERT: D 155 ILE cc_start: 0.9375 (mt) cc_final: 0.9125 (tt) REVERT: D 219 GLN cc_start: 0.9058 (mt0) cc_final: 0.8768 (mt0) outliers start: 23 outliers final: 8 residues processed: 223 average time/residue: 0.0933 time to fit residues: 28.3269 Evaluate side-chains 187 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 556 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.081571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068463 restraints weight = 34755.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070262 restraints weight = 22088.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071532 restraints weight = 16096.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072477 restraints weight = 12782.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.073158 restraints weight = 10718.736| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8336 Z= 0.229 Angle : 0.682 11.458 11263 Z= 0.359 Chirality : 0.043 0.171 1242 Planarity : 0.005 0.049 1435 Dihedral : 12.090 112.438 1198 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.86 % Allowed : 16.69 % Favored : 79.46 % 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: 0.67 (0.26), residues: 1007 helix: 1.41 (0.20), residues: 606 sheet: -0.55 (0.60), residues: 62 loop : -1.11 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 563 TYR 0.012 0.002 TYR C 179 PHE 0.023 0.002 PHE D 196 TRP 0.011 0.002 TRP D 59 HIS 0.007 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 ( 8336) covalent geometry : angle 0.68220 / 0.36 (11263) hydrogen bonds : bond 0.04585 / 3.05 ( 507) hydrogen bonds : angle 4.78711 / 3.49 ( 1500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8883 (mmm) cc_final: 0.8547 (mmm) REVERT: A 530 ASP cc_start: 0.8870 (m-30) cc_final: 0.8599 (m-30) REVERT: A 560 MET cc_start: 0.9071 (mtp) cc_final: 0.8316 (mtp) REVERT: B 185 LYS cc_start: 0.8283 (tptt) cc_final: 0.7740 (tppt) REVERT: C 15 GLN cc_start: 0.9509 (mt0) cc_final: 0.9298 (pt0) REVERT: C 129 LEU cc_start: 0.9597 (mt) cc_final: 0.9118 (mt) REVERT: C 219 GLN cc_start: 0.9165 (tp40) cc_final: 0.8951 (tp-100) REVERT: D 14 GLU cc_start: 0.8823 (tt0) cc_final: 0.8586 (tp30) REVERT: D 22 MET cc_start: 0.7702 (ptm) cc_final: 0.7186 (ptm) REVERT: D 139 ASN cc_start: 0.9383 (m-40) cc_final: 0.9066 (m-40) REVERT: D 155 ILE cc_start: 0.9417 (mt) cc_final: 0.9162 (tt) outliers start: 34 outliers final: 24 residues processed: 200 average time/residue: 0.0920 time to fit residues: 25.1793 Evaluate side-chains 183 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 444 GLN A 477 HIS C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.084815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071796 restraints weight = 30475.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.073523 restraints weight = 20141.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074767 restraints weight = 14959.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.075689 restraints weight = 12042.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076390 restraints weight = 10138.743| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8336 Z= 0.138 Angle : 0.652 11.474 11263 Z= 0.330 Chirality : 0.042 0.192 1242 Planarity : 0.004 0.047 1435 Dihedral : 10.848 104.165 1196 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.75 % Allowed : 18.73 % Favored : 77.53 % 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: 0.78 (0.26), residues: 1007 helix: 1.55 (0.20), residues: 604 sheet: -0.20 (0.67), residues: 51 loop : -1.20 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 563 TYR 0.019 0.001 TYR C 211 PHE 0.021 0.002 PHE A 559 TRP 0.017 0.002 TRP A 496 HIS 0.005 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8336) covalent geometry : angle 0.65195 / 0.33 (11263) hydrogen bonds : bond 0.04213 / 2.78 ( 507) hydrogen bonds : angle 4.60537 / 3.34 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8805 (mmm) cc_final: 0.8502 (mmm) REVERT: A 518 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6350 (tpm170) REVERT: A 530 ASP cc_start: 0.8793 (m-30) cc_final: 0.8555 (m-30) REVERT: A 560 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8464 (mmm) REVERT: B 185 LYS cc_start: 0.8134 (tptt) cc_final: 0.7560 (tppt) REVERT: B 187 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5574 (ptp) REVERT: B 230 MET cc_start: 0.4435 (ttm) cc_final: 0.3642 (ttt) REVERT: C 59 TRP cc_start: 0.8582 (t60) cc_final: 0.8314 (t60) REVERT: C 211 TYR cc_start: 0.7179 (t80) cc_final: 0.6731 (t80) REVERT: C 219 GLN cc_start: 0.9134 (tp40) cc_final: 0.8904 (tp-100) REVERT: D 14 GLU cc_start: 0.8824 (tt0) cc_final: 0.8487 (tp30) REVERT: D 22 MET cc_start: 0.7635 (ptm) cc_final: 0.6948 (ptm) REVERT: D 139 ASN cc_start: 0.9362 (m-40) cc_final: 0.9030 (m-40) REVERT: D 194 GLN cc_start: 0.9026 (pt0) cc_final: 0.8825 (tp-100) REVERT: D 219 GLN cc_start: 0.9051 (mt0) cc_final: 0.8831 (mt0) outliers start: 33 outliers final: 19 residues processed: 195 average time/residue: 0.0774 time to fit residues: 21.6604 Evaluate side-chains 178 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0570 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072448 restraints weight = 34721.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.074375 restraints weight = 21840.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075803 restraints weight = 15778.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.076794 restraints weight = 12371.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077601 restraints weight = 10282.107| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8336 Z= 0.133 Angle : 0.667 14.109 11263 Z= 0.332 Chirality : 0.043 0.337 1242 Planarity : 0.004 0.047 1435 Dihedral : 10.058 90.913 1196 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.72 % Allowed : 20.32 % Favored : 76.96 % 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: 0.78 (0.26), residues: 1007 helix: 1.52 (0.20), residues: 612 sheet: -0.36 (0.66), residues: 51 loop : -1.19 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 563 TYR 0.024 0.001 TYR C 211 PHE 0.024 0.002 PHE A 559 TRP 0.009 0.001 TRP A 511 HIS 0.008 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 8336) covalent geometry : angle 0.66678 / 0.33 (11263) hydrogen bonds : bond 0.04082 / 2.68 ( 507) hydrogen bonds : angle 4.55660 / 3.32 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8787 (mmm) cc_final: 0.8446 (mmm) REVERT: A 518 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.5973 (tpm170) REVERT: B 185 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7348 (tppt) REVERT: B 187 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5593 (ptp) REVERT: B 230 MET cc_start: 0.4550 (ttm) cc_final: 0.3761 (ttt) REVERT: C 15 GLN cc_start: 0.9355 (mt0) cc_final: 0.9038 (pt0) REVERT: C 59 TRP cc_start: 0.8555 (t60) cc_final: 0.8208 (t60) REVERT: C 127 ARG cc_start: 0.8954 (ttp80) cc_final: 0.8677 (ttp-110) REVERT: C 215 THR cc_start: 0.8680 (t) cc_final: 0.8316 (p) REVERT: C 219 GLN cc_start: 0.9121 (tp40) cc_final: 0.8893 (tp-100) REVERT: D 14 GLU cc_start: 0.8782 (tt0) cc_final: 0.8513 (tp30) REVERT: D 22 MET cc_start: 0.7597 (ptm) cc_final: 0.7197 (ptm) REVERT: D 139 ASN cc_start: 0.9323 (m-40) cc_final: 0.8990 (m-40) REVERT: D 194 GLN cc_start: 0.9032 (pt0) cc_final: 0.8780 (tp-100) REVERT: D 219 GLN cc_start: 0.9132 (mt0) cc_final: 0.8806 (mt0) outliers start: 24 outliers final: 15 residues processed: 186 average time/residue: 0.0868 time to fit residues: 22.5769 Evaluate side-chains 177 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 153 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.084061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070933 restraints weight = 34531.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.072703 restraints weight = 22174.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.074013 restraints weight = 16211.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074938 restraints weight = 12878.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075593 restraints weight = 10794.762| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8336 Z= 0.193 Angle : 0.682 12.967 11263 Z= 0.349 Chirality : 0.043 0.241 1242 Planarity : 0.004 0.048 1435 Dihedral : 9.409 79.842 1196 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.86 % Allowed : 20.32 % Favored : 75.82 % 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: 0.60 (0.26), residues: 1007 helix: 1.35 (0.20), residues: 611 sheet: -0.33 (0.67), residues: 51 loop : -1.21 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 222 TYR 0.018 0.002 TYR B 125 PHE 0.024 0.002 PHE A 559 TRP 0.011 0.002 TRP A 511 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 8336) covalent geometry : angle 0.68166 / 0.35 (11263) hydrogen bonds : bond 0.04243 / 2.77 ( 507) hydrogen bonds : angle 4.66944 / 3.40 ( 1500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8960 (mmm) cc_final: 0.8634 (mmm) REVERT: A 518 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6333 (tpm170) REVERT: B 94 MET cc_start: 0.7859 (pmm) cc_final: 0.7532 (pmm) REVERT: B 125 TYR cc_start: 0.8811 (m-80) cc_final: 0.8606 (m-80) REVERT: B 185 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7237 (tppt) REVERT: B 187 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5709 (ptp) REVERT: C 15 GLN cc_start: 0.9432 (mt0) cc_final: 0.9149 (pt0) REVERT: C 59 TRP cc_start: 0.8662 (t60) cc_final: 0.8440 (t60) REVERT: D 14 GLU cc_start: 0.8910 (tt0) cc_final: 0.8631 (tp30) REVERT: D 22 MET cc_start: 0.7715 (ptm) cc_final: 0.7206 (ptm) REVERT: D 139 ASN cc_start: 0.9328 (m-40) cc_final: 0.8921 (m-40) REVERT: D 146 GLN cc_start: 0.8729 (mt0) cc_final: 0.8415 (mt0) REVERT: D 155 ILE cc_start: 0.9476 (mt) cc_final: 0.9140 (tt) REVERT: D 194 GLN cc_start: 0.9057 (pt0) cc_final: 0.8787 (tp-100) REVERT: D 219 GLN cc_start: 0.9089 (mt0) cc_final: 0.8759 (mt0) outliers start: 34 outliers final: 27 residues processed: 179 average time/residue: 0.0811 time to fit residues: 20.5937 Evaluate side-chains 186 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 206 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 29 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.083843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.070880 restraints weight = 34285.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072673 restraints weight = 21553.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.074017 restraints weight = 15609.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.074969 restraints weight = 12265.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.075458 restraints weight = 10194.353| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8336 Z= 0.135 Angle : 0.694 14.710 11263 Z= 0.344 Chirality : 0.043 0.354 1242 Planarity : 0.004 0.047 1435 Dihedral : 7.955 58.592 1196 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.72 % Allowed : 21.68 % Favored : 75.60 % 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: 0.67 (0.26), residues: 1007 helix: 1.44 (0.20), residues: 612 sheet: -0.74 (0.61), residues: 58 loop : -1.19 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 83 TYR 0.033 0.001 TYR C 211 PHE 0.018 0.002 PHE A 559 TRP 0.008 0.001 TRP C 228 HIS 0.007 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 8336) covalent geometry : angle 0.69367 / 0.34 (11263) hydrogen bonds : bond 0.03992 / 2.60 ( 507) hydrogen bonds : angle 4.53423 / 3.28 ( 1500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8779 (mmm) cc_final: 0.8520 (mmm) REVERT: A 556 GLN cc_start: 0.8402 (tt0) cc_final: 0.7962 (tm-30) REVERT: B 94 MET cc_start: 0.7727 (pmm) cc_final: 0.7410 (pmm) REVERT: B 125 TYR cc_start: 0.8781 (m-80) cc_final: 0.8504 (m-80) REVERT: B 185 LYS cc_start: 0.7961 (tptt) cc_final: 0.7300 (tppt) REVERT: B 187 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.5485 (ptp) REVERT: B 230 MET cc_start: 0.4382 (ttm) cc_final: 0.3521 (ttt) REVERT: C 15 GLN cc_start: 0.9407 (mt0) cc_final: 0.9102 (pt0) REVERT: C 22 MET cc_start: 0.7856 (tpt) cc_final: 0.7601 (tpt) REVERT: C 59 TRP cc_start: 0.8599 (t60) cc_final: 0.8327 (t60) REVERT: C 127 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8694 (ttp-110) REVERT: D 14 GLU cc_start: 0.8883 (tt0) cc_final: 0.8555 (tp30) REVERT: D 22 MET cc_start: 0.7719 (ptm) cc_final: 0.7017 (ptp) REVERT: D 139 ASN cc_start: 0.9351 (m-40) cc_final: 0.8951 (m-40) REVERT: D 146 GLN cc_start: 0.8576 (mt0) cc_final: 0.8177 (mt0) REVERT: D 194 GLN cc_start: 0.9118 (pt0) cc_final: 0.8881 (tp-100) REVERT: D 219 GLN cc_start: 0.9129 (mt0) cc_final: 0.8822 (mt0) outliers start: 24 outliers final: 16 residues processed: 179 average time/residue: 0.0819 time to fit residues: 20.8429 Evaluate side-chains 181 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 0.0470 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.082923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070118 restraints weight = 34251.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071889 restraints weight = 21750.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073184 restraints weight = 15805.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074208 restraints weight = 12370.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.074914 restraints weight = 10233.073| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8336 Z= 0.142 Angle : 0.713 13.947 11263 Z= 0.351 Chirality : 0.043 0.308 1242 Planarity : 0.004 0.048 1435 Dihedral : 7.361 58.293 1196 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.72 % Allowed : 21.79 % Favored : 75.48 % 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 (0.26), residues: 1007 helix: 1.44 (0.21), residues: 612 sheet: -0.87 (0.60), residues: 58 loop : -1.20 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 83 TYR 0.013 0.001 TYR C 211 PHE 0.018 0.001 PHE A 559 TRP 0.031 0.002 TRP D 228 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8336) covalent geometry : angle 0.71338 / 0.35 (11263) hydrogen bonds : bond 0.04005 / 2.60 ( 507) hydrogen bonds : angle 4.59763 / 3.32 ( 1500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8843 (mmm) cc_final: 0.8515 (mmm) REVERT: A 556 GLN cc_start: 0.8427 (tt0) cc_final: 0.8021 (tm-30) REVERT: B 94 MET cc_start: 0.7760 (pmm) cc_final: 0.7521 (pmm) REVERT: B 185 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7295 (tppt) REVERT: B 187 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5458 (ptp) REVERT: B 227 ARG cc_start: 0.5852 (ppt170) cc_final: 0.5481 (ptt90) REVERT: B 230 MET cc_start: 0.4392 (ttm) cc_final: 0.3547 (ttt) REVERT: C 15 GLN cc_start: 0.9407 (mt0) cc_final: 0.9089 (pt0) REVERT: C 59 TRP cc_start: 0.8566 (t60) cc_final: 0.8284 (t60) REVERT: C 127 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8691 (ttp-110) REVERT: D 14 GLU cc_start: 0.8848 (tt0) cc_final: 0.8610 (tp30) REVERT: D 22 MET cc_start: 0.7717 (ptm) cc_final: 0.7298 (ptm) REVERT: D 139 ASN cc_start: 0.9317 (m-40) cc_final: 0.9004 (t0) REVERT: D 194 GLN cc_start: 0.9053 (pt0) cc_final: 0.8822 (tp-100) REVERT: D 219 GLN cc_start: 0.9077 (mt0) cc_final: 0.8831 (mt0) outliers start: 24 outliers final: 21 residues processed: 175 average time/residue: 0.0821 time to fit residues: 20.3196 Evaluate side-chains 187 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN D 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.082917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070070 restraints weight = 34013.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071825 restraints weight = 21660.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073050 restraints weight = 15740.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073985 restraints weight = 12467.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074696 restraints weight = 10427.839| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8336 Z= 0.159 Angle : 0.741 14.549 11263 Z= 0.364 Chirality : 0.044 0.379 1242 Planarity : 0.004 0.048 1435 Dihedral : 7.074 56.178 1196 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.61 % Allowed : 22.36 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1007 helix: 1.39 (0.21), residues: 612 sheet: -0.98 (0.61), residues: 58 loop : -1.22 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 83 TYR 0.030 0.001 TYR C 211 PHE 0.020 0.001 PHE A 559 TRP 0.024 0.002 TRP D 228 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 8336) covalent geometry : angle 0.74098 / 0.36 (11263) hydrogen bonds : bond 0.04018 / 2.65 ( 507) hydrogen bonds : angle 4.64235 / 3.36 ( 1500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8886 (mmm) cc_final: 0.8563 (mmm) REVERT: A 556 GLN cc_start: 0.8389 (tt0) cc_final: 0.7950 (tm-30) REVERT: B 94 MET cc_start: 0.7752 (pmm) cc_final: 0.7516 (pmm) REVERT: B 185 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7290 (tppt) REVERT: B 187 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5442 (ptp) REVERT: B 227 ARG cc_start: 0.5920 (ppt170) cc_final: 0.5561 (ptt90) REVERT: B 230 MET cc_start: 0.4481 (ttm) cc_final: 0.3607 (ttt) REVERT: C 15 GLN cc_start: 0.9411 (mt0) cc_final: 0.9096 (pt0) REVERT: C 59 TRP cc_start: 0.8573 (t60) cc_final: 0.8282 (t60) REVERT: C 127 ARG cc_start: 0.8987 (ttp80) cc_final: 0.8687 (ttp-110) REVERT: D 14 GLU cc_start: 0.8881 (tt0) cc_final: 0.8650 (tp30) REVERT: D 22 MET cc_start: 0.7739 (ptm) cc_final: 0.7305 (ptm) REVERT: D 139 ASN cc_start: 0.9306 (m-40) cc_final: 0.9003 (t0) REVERT: D 194 GLN cc_start: 0.9064 (pt0) cc_final: 0.8821 (tp-100) REVERT: D 219 GLN cc_start: 0.9108 (mt0) cc_final: 0.8853 (mt0) outliers start: 23 outliers final: 20 residues processed: 175 average time/residue: 0.0805 time to fit residues: 20.1659 Evaluate side-chains 186 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS C 8 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN D 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.084876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.071853 restraints weight = 33384.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073625 restraints weight = 21370.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074930 restraints weight = 15529.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.075875 restraints weight = 12223.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076360 restraints weight = 10155.091| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8336 Z= 0.140 Angle : 0.767 15.558 11263 Z= 0.371 Chirality : 0.045 0.398 1242 Planarity : 0.004 0.047 1435 Dihedral : 6.711 52.325 1196 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.50 % Allowed : 22.93 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1007 helix: 1.39 (0.20), residues: 612 sheet: -1.02 (0.60), residues: 58 loop : -1.20 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.026 0.001 TYR C 211 PHE 0.019 0.002 PHE A 559 TRP 0.023 0.002 TRP D 228 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8336) covalent geometry : angle 0.76677 / 0.37 (11263) hydrogen bonds : bond 0.04027 / 2.64 ( 507) hydrogen bonds : angle 4.63680 / 3.37 ( 1500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8852 (mmm) cc_final: 0.8543 (mmm) REVERT: A 556 GLN cc_start: 0.8402 (tt0) cc_final: 0.7909 (tm-30) REVERT: B 185 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7326 (tppt) REVERT: B 187 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5398 (ptp) REVERT: B 227 ARG cc_start: 0.5922 (ppt170) cc_final: 0.5606 (ptt90) REVERT: B 230 MET cc_start: 0.4339 (ttm) cc_final: 0.3521 (ttt) REVERT: B 235 LEU cc_start: 0.8347 (tp) cc_final: 0.7866 (tp) REVERT: C 15 GLN cc_start: 0.9394 (mt0) cc_final: 0.9074 (pt0) REVERT: C 59 TRP cc_start: 0.8543 (t60) cc_final: 0.8234 (t60) REVERT: C 127 ARG cc_start: 0.8943 (ttp80) cc_final: 0.8636 (ttp-110) REVERT: C 186 ASP cc_start: 0.9177 (p0) cc_final: 0.8851 (p0) REVERT: C 190 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8992 (tm-30) REVERT: D 14 GLU cc_start: 0.8853 (tt0) cc_final: 0.8554 (tp30) REVERT: D 22 MET cc_start: 0.7739 (ptm) cc_final: 0.7010 (ptp) REVERT: D 139 ASN cc_start: 0.9294 (m-40) cc_final: 0.9010 (t0) REVERT: D 194 GLN cc_start: 0.9072 (pt0) cc_final: 0.8844 (tp-100) REVERT: D 219 GLN cc_start: 0.9100 (mt0) cc_final: 0.8857 (mt0) outliers start: 22 outliers final: 17 residues processed: 180 average time/residue: 0.0836 time to fit residues: 21.2417 Evaluate side-chains 185 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN D 146 GLN ** D 173 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 = 0.3667 r_free = 0.3667 target = 0.083021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070148 restraints weight = 33760.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.071882 restraints weight = 21640.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.073198 restraints weight = 15810.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074126 restraints weight = 12461.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.074853 restraints weight = 10396.848| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8336 Z= 0.143 Angle : 0.781 15.263 11263 Z= 0.383 Chirality : 0.046 0.391 1242 Planarity : 0.005 0.075 1435 Dihedral : 6.591 53.081 1196 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.50 % Allowed : 22.93 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1007 helix: 1.30 (0.20), residues: 613 sheet: -1.00 (0.62), residues: 57 loop : -1.16 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 9 TYR 0.023 0.001 TYR C 211 PHE 0.020 0.001 PHE A 559 TRP 0.021 0.002 TRP D 228 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8336) covalent geometry : angle 0.78145 / 0.38 (11263) hydrogen bonds : bond 0.04086 / 2.73 ( 507) hydrogen bonds : angle 4.69372 / 3.40 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1538.33 seconds wall clock time: 27 minutes 34.01 seconds (1654.01 seconds total)