Starting phenix.real_space_refine on Wed Feb 4 02:07:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmr_48401/02_2026/9mmr_48401.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmr_48401/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmr_48401/02_2026/9mmr_48401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmr_48401/02_2026/9mmr_48401.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmr_48401/02_2026/9mmr_48401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmr_48401/02_2026/9mmr_48401.cif" } 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-2.0-5952/lib/python3.9/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: 2.01, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 326.5 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: 0.27 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: 1.48 Time building geometry restraints manager: 1.14 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=" 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 bond pdb=" N ILE B 196 " pdb=" CA ILE B 196 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.20e-02 6.94e+03 7.41e+00 bond pdb=" N HIS B 188 " pdb=" CA HIS B 188 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.95e+00 bond pdb=" N ASN D 173 " pdb=" CA ASN D 173 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.63e+00 bond pdb=" N TYR B 240 " pdb=" CA TYR B 240 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.34e+00 ... (remaining 8331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11116 2.39 - 4.78: 137 4.78 - 7.17: 8 7.17 - 9.57: 1 9.57 - 11.96: 1 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=" 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=" 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 angle pdb=" CA THR C 226 " pdb=" CB THR C 226 " pdb=" OG1 THR C 226 " ideal model delta sigma weight residual 109.60 104.82 4.78 1.50e+00 4.44e-01 1.02e+01 angle pdb=" CA THR C 215 " pdb=" CB THR C 215 " pdb=" OG1 THR C 215 " ideal model delta sigma weight residual 109.60 104.91 4.69 1.50e+00 4.44e-01 9.77e+00 ... (remaining 11258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.66: 5034 30.66 - 61.32: 66 61.32 - 91.98: 4 91.98 - 122.64: 1 122.64 - 153.30: 1 Dihedral angle restraints: 5106 sinusoidal: 2117 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=" O1B 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 68.91 -84.39 153.30 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O1A AGS A 701 " pdb=" O3A AGS A 701 " pdb=" PA AGS A 701 " pdb=" PB AGS A 701 " ideal model delta sinusoidal sigma weight residual 292.27 172.60 119.67 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 847 0.034 - 0.069: 284 0.069 - 0.103: 85 0.103 - 0.138: 27 0.138 - 0.172: 3 Chirality restraints: 1246 Sorted by residual: 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 chirality pdb=" CA ARG C 222 " pdb=" N ARG C 222 " pdb=" C ARG C 222 " pdb=" CB ARG C 222 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ILE A 376 " pdb=" N ILE A 376 " pdb=" C ILE A 376 " pdb=" CB ILE A 376 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1243 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: 4.090 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 15.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 0.072 8336 Z= 0.259 Angle : 0.650 11.958 11263 Z= 0.393 Chirality : 0.040 0.172 1246 Planarity : 0.009 0.314 1435 Dihedral : 11.533 153.300 3174 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 covalent geometry : bond 0.00461 ( 8336) covalent geometry : angle 0.65027 (11263) hydrogen bonds : bond 0.13424 ( 507) hydrogen bonds : angle 5.56415 ( 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 : 0.397 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: 0.1241 time to fit residues: 51.0050 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 : 0.343 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 444 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 610 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3695 r_free = 0.3695 target = 0.086413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073183 restraints weight = 33763.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074949 restraints weight = 22165.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076233 restraints weight = 16382.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077181 restraints weight = 13061.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077880 restraints weight = 10997.436| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8336 Z= 0.162 Angle : 0.678 9.240 11263 Z= 0.353 Chirality : 0.042 0.164 1246 Planarity : 0.004 0.051 1435 Dihedral : 9.855 159.269 1168 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.50 % Allowed : 17.14 % Favored : 80.36 % 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: 1.80 (0.21), residues: 608 sheet: -0.45 (0.57), residues: 58 loop : -0.91 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 450 TYR 0.015 0.002 TYR D 128 PHE 0.016 0.002 PHE D 196 TRP 0.013 0.001 TRP D 59 HIS 0.007 0.001 HIS D 164 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8336) covalent geometry : angle 0.67758 (11263) hydrogen bonds : bond 0.04922 ( 507) hydrogen bonds : angle 4.65478 ( 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 235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.347 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: A 378 LYS cc_start: 0.8270 (mttm) cc_final: 0.7913 (pttm) REVERT: A 401 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7625 (tpp80) REVERT: A 622 GLU cc_start: 0.8482 (tp30) cc_final: 0.8280 (tp30) REVERT: B 94 MET cc_start: 0.7472 (ptp) cc_final: 0.7230 (ptm) REVERT: B 142 CYS cc_start: 0.8406 (m) cc_final: 0.7022 (m) REVERT: B 143 MET cc_start: 0.8112 (ptt) cc_final: 0.7570 (ptp) REVERT: B 185 LYS cc_start: 0.8462 (tptt) cc_final: 0.8014 (tppt) REVERT: B 236 GLN cc_start: 0.8581 (mt0) cc_final: 0.8307 (mm-40) REVERT: C 8 GLN cc_start: 0.8999 (pp30) cc_final: 0.8759 (pp30) REVERT: C 26 MET cc_start: 0.9118 (mmm) cc_final: 0.8282 (mmm) REVERT: C 59 TRP cc_start: 0.8560 (t60) cc_final: 0.8227 (t60) REVERT: C 198 ASP cc_start: 0.8785 (t0) cc_final: 0.8573 (t0) REVERT: C 215 THR cc_start: 0.8602 (t) cc_final: 0.8401 (p) REVERT: D 14 GLU cc_start: 0.8731 (tt0) cc_final: 0.8419 (tp30) REVERT: D 22 MET cc_start: 0.7530 (ptm) cc_final: 0.7275 (ptm) REVERT: D 139 ASN cc_start: 0.9364 (m-40) cc_final: 0.9042 (m-40) REVERT: D 155 ILE cc_start: 0.9364 (mt) cc_final: 0.9114 (tt) REVERT: D 219 GLN cc_start: 0.9045 (mt0) cc_final: 0.8757 (mt0) outliers start: 22 outliers final: 8 residues processed: 222 average time/residue: 0.0969 time to fit residues: 29.1370 Evaluate side-chains 184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 8.9990 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 556 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.085094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071896 restraints weight = 34204.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073646 restraints weight = 22283.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074863 restraints weight = 16431.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075706 restraints weight = 13152.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.076396 restraints weight = 11283.205| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8336 Z= 0.206 Angle : 0.677 11.471 11263 Z= 0.358 Chirality : 0.042 0.146 1246 Planarity : 0.005 0.049 1435 Dihedral : 9.217 154.816 1162 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.63 % Allowed : 17.25 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1007 helix: 1.41 (0.20), residues: 607 sheet: -0.44 (0.62), residues: 57 loop : -1.11 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 563 TYR 0.013 0.001 TYR C 179 PHE 0.026 0.002 PHE D 196 TRP 0.009 0.002 TRP D 59 HIS 0.005 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8336) covalent geometry : angle 0.67719 (11263) hydrogen bonds : bond 0.04576 ( 507) hydrogen bonds : angle 4.76448 ( 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 212 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.350 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: 0.8653 (mmm) cc_final: 0.8383 (mmm) REVERT: A 530 ASP cc_start: 0.8862 (m-30) cc_final: 0.8612 (m-30) REVERT: A 560 MET cc_start: 0.9061 (mtp) cc_final: 0.8363 (mtp) REVERT: B 184 HIS cc_start: 0.8232 (m-70) cc_final: 0.7560 (m-70) REVERT: B 185 LYS cc_start: 0.8205 (tptt) cc_final: 0.7638 (tppt) REVERT: C 59 TRP cc_start: 0.8741 (t60) cc_final: 0.8539 (t60) REVERT: C 88 LYS cc_start: 0.9434 (mttp) cc_final: 0.9230 (mttp) REVERT: C 129 LEU cc_start: 0.9605 (mt) cc_final: 0.9126 (mt) REVERT: C 215 THR cc_start: 0.8663 (t) cc_final: 0.8377 (p) REVERT: C 219 GLN cc_start: 0.9133 (tp40) cc_final: 0.8900 (tp-100) REVERT: D 14 GLU cc_start: 0.8852 (tt0) cc_final: 0.8589 (tp30) REVERT: D 22 MET cc_start: 0.7654 (ptm) cc_final: 0.7127 (ptm) REVERT: D 139 ASN cc_start: 0.9393 (m-40) cc_final: 0.9070 (m-40) REVERT: D 155 ILE cc_start: 0.9431 (mt) cc_final: 0.9166 (tt) REVERT: D 229 THR cc_start: 0.8801 (m) cc_final: 0.8599 (p) outliers start: 32 outliers final: 21 residues processed: 197 average time/residue: 0.0986 time to fit residues: 26.3078 Evaluate side-chains 178 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 555 ASP Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 171 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 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: 4.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.070229 restraints weight = 34076.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072041 restraints weight = 22221.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073313 restraints weight = 16456.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074237 restraints weight = 13049.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074932 restraints weight = 11021.082| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8336 Z= 0.176 Angle : 0.654 10.482 11263 Z= 0.340 Chirality : 0.042 0.203 1246 Planarity : 0.004 0.049 1435 Dihedral : 9.146 155.369 1160 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.31 % Allowed : 18.84 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1007 helix: 1.35 (0.20), residues: 606 sheet: -0.33 (0.67), residues: 51 loop : -1.21 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 563 TYR 0.029 0.001 TYR C 211 PHE 0.022 0.002 PHE B 360 TRP 0.017 0.002 TRP A 496 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8336) covalent geometry : angle 0.65378 (11263) hydrogen bonds : bond 0.04394 ( 507) hydrogen bonds : angle 4.72717 ( 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 202 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.344 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 371 ASP cc_start: 0.7540 (t70) cc_final: 0.7190 (t0) REVERT: A 409 MET cc_start: 0.8116 (mtp) cc_final: 0.7896 (mtt) REVERT: A 518 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6134 (tpm170) REVERT: A 530 ASP cc_start: 0.8877 (m-30) cc_final: 0.8620 (m-30) REVERT: A 559 PHE cc_start: 0.8133 (t80) cc_final: 0.7837 (t80) REVERT: A 560 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8608 (mmt) REVERT: B 185 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7520 (tppt) REVERT: B 230 MET cc_start: 0.4761 (ttm) cc_final: 0.3951 (ttt) REVERT: C 15 GLN cc_start: 0.9364 (mt0) cc_final: 0.9124 (pt0) REVERT: C 59 TRP cc_start: 0.8743 (t60) cc_final: 0.8521 (t60) REVERT: C 211 TYR cc_start: 0.7262 (t80) cc_final: 0.6585 (t80) REVERT: C 219 GLN cc_start: 0.9183 (tp40) cc_final: 0.8972 (tp-100) REVERT: D 14 GLU cc_start: 0.8893 (tt0) cc_final: 0.8594 (tp30) REVERT: D 22 MET cc_start: 0.7687 (ptm) cc_final: 0.7216 (ptm) REVERT: D 139 ASN cc_start: 0.9390 (m-40) cc_final: 0.9056 (m-40) REVERT: D 155 ILE cc_start: 0.9436 (mt) cc_final: 0.9195 (tp) REVERT: D 219 GLN cc_start: 0.8976 (mt0) cc_final: 0.8679 (mt0) REVERT: D 222 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8799 (tpp-160) outliers start: 38 outliers final: 24 residues processed: 185 average time/residue: 0.0792 time to fit residues: 21.0310 Evaluate side-chains 181 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 419 ILE 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 518 ARG Chi-restraints excluded: chain A residue 560 MET 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 239 HIS Chi-restraints excluded: chain B residue 242 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 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 D residue 21 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 222 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.083116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069560 restraints weight = 35489.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071353 restraints weight = 22795.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072721 restraints weight = 16676.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073659 restraints weight = 13195.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.074116 restraints weight = 11110.447| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8336 Z= 0.155 Angle : 0.636 11.236 11263 Z= 0.329 Chirality : 0.043 0.371 1246 Planarity : 0.004 0.065 1435 Dihedral : 9.062 156.194 1160 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.86 % Allowed : 19.52 % Favored : 76.62 % 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: 0.58 (0.26), residues: 1007 helix: 1.37 (0.20), residues: 612 sheet: -0.37 (0.67), residues: 51 loop : -1.27 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 563 TYR 0.027 0.001 TYR C 211 PHE 0.027 0.002 PHE B 360 TRP 0.011 0.001 TRP D 59 HIS 0.005 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8336) covalent geometry : angle 0.63627 (11263) hydrogen bonds : bond 0.04206 ( 507) hydrogen bonds : angle 4.63656 ( 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 196 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 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: A 365 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7579 (mtmm) REVERT: A 518 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6397 (tpm170) REVERT: B 185 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7296 (tppt) REVERT: B 230 MET cc_start: 0.4677 (ttm) cc_final: 0.3860 (ttt) REVERT: C 59 TRP cc_start: 0.8679 (t60) cc_final: 0.8472 (t60) REVERT: C 219 GLN cc_start: 0.9188 (tp40) cc_final: 0.8986 (tp-100) REVERT: D 14 GLU cc_start: 0.8878 (tt0) cc_final: 0.8584 (tp30) REVERT: D 22 MET cc_start: 0.7653 (ptm) cc_final: 0.7185 (ptm) REVERT: D 139 ASN cc_start: 0.9340 (m-40) cc_final: 0.8974 (m-40) REVERT: D 155 ILE cc_start: 0.9415 (mt) cc_final: 0.9182 (tp) outliers start: 34 outliers final: 20 residues processed: 183 average time/residue: 0.0833 time to fit residues: 21.7926 Evaluate side-chains 176 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 403 VAL 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 506 THR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 238 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 14 optimal weight: 0.0010 chunk 77 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.083105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069757 restraints weight = 34670.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071400 restraints weight = 22416.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072694 restraints weight = 16523.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073627 restraints weight = 13126.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.074350 restraints weight = 11032.812| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8336 Z= 0.174 Angle : 0.674 13.138 11263 Z= 0.344 Chirality : 0.044 0.321 1246 Planarity : 0.005 0.081 1435 Dihedral : 9.103 156.770 1160 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.48 (0.26), residues: 1007 helix: 1.28 (0.20), residues: 610 sheet: -0.52 (0.66), residues: 51 loop : -1.26 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 222 TYR 0.011 0.001 TYR C 211 PHE 0.023 0.002 PHE B 360 TRP 0.011 0.001 TRP D 59 HIS 0.007 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8336) covalent geometry : angle 0.67434 (11263) hydrogen bonds : bond 0.04236 ( 507) hydrogen bonds : angle 4.69606 ( 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 192 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.350 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 365 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7674 (mtmm) REVERT: A 518 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6098 (tpm170) REVERT: B 185 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7355 (tppt) REVERT: C 59 TRP cc_start: 0.8764 (t60) cc_final: 0.8477 (t60) REVERT: C 219 GLN cc_start: 0.9221 (tp40) cc_final: 0.9020 (tp-100) REVERT: D 14 GLU cc_start: 0.8950 (tt0) cc_final: 0.8530 (tp30) REVERT: D 22 MET cc_start: 0.7746 (ptm) cc_final: 0.7324 (ptm) REVERT: D 67 GLN cc_start: 0.9373 (mm-40) cc_final: 0.9129 (mp10) REVERT: D 139 ASN cc_start: 0.9383 (m-40) cc_final: 0.8978 (m-40) REVERT: D 155 ILE cc_start: 0.9467 (mt) cc_final: 0.9210 (tp) outliers start: 34 outliers final: 25 residues processed: 177 average time/residue: 0.0833 time to fit residues: 21.2490 Evaluate side-chains 177 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 403 VAL 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 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 SER 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 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 166 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 34 VAL 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: 9.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 190 GLN D 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.083301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069815 restraints weight = 35067.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071622 restraints weight = 22290.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.072968 restraints weight = 16249.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.073970 restraints weight = 12821.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.074705 restraints weight = 10674.063| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8336 Z= 0.137 Angle : 0.673 13.731 11263 Z= 0.340 Chirality : 0.044 0.379 1246 Planarity : 0.005 0.067 1435 Dihedral : 9.044 157.084 1160 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.41 % Allowed : 21.68 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1007 helix: 1.34 (0.21), residues: 613 sheet: -0.52 (0.66), residues: 51 loop : -1.27 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 167 TYR 0.029 0.001 TYR C 211 PHE 0.028 0.002 PHE B 360 TRP 0.010 0.001 TRP D 59 HIS 0.008 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8336) covalent geometry : angle 0.67255 (11263) hydrogen bonds : bond 0.04100 ( 507) hydrogen bonds : angle 4.58899 ( 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: 30 poor density : 162 time to evaluate : 0.258 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 518 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6269 (tpm170) REVERT: B 125 TYR cc_start: 0.8915 (m-80) cc_final: 0.8692 (m-80) REVERT: B 185 LYS cc_start: 0.7888 (tptt) cc_final: 0.7229 (tppt) REVERT: B 198 VAL cc_start: 0.8806 (m) cc_final: 0.8569 (m) REVERT: B 230 MET cc_start: 0.4483 (ttm) cc_final: 0.3675 (ttt) REVERT: C 15 GLN cc_start: 0.9370 (mt0) cc_final: 0.9046 (pt0) REVERT: D 14 GLU cc_start: 0.8810 (tt0) cc_final: 0.8451 (tp30) REVERT: D 22 MET cc_start: 0.7597 (ptm) cc_final: 0.7177 (ptm) REVERT: D 139 ASN cc_start: 0.9224 (m-40) cc_final: 0.8818 (t0) outliers start: 30 outliers final: 23 residues processed: 176 average time/residue: 0.0694 time to fit residues: 17.6900 Evaluate side-chains 181 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 438 THR Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 174 ILE 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 212 LYS Chi-restraints excluded: chain C residue 221 LEU 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 194 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 195 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.083568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070558 restraints weight = 33790.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072299 restraints weight = 21589.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073574 restraints weight = 15742.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074466 restraints weight = 12425.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.074863 restraints weight = 10532.813| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8336 Z= 0.138 Angle : 0.686 14.204 11263 Z= 0.346 Chirality : 0.043 0.340 1246 Planarity : 0.004 0.055 1435 Dihedral : 8.985 155.095 1160 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.84 % Allowed : 22.47 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.26), residues: 1007 helix: 1.39 (0.20), residues: 607 sheet: -0.94 (0.61), residues: 58 loop : -1.23 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 234 TYR 0.018 0.001 TYR C 125 PHE 0.022 0.002 PHE B 360 TRP 0.018 0.001 TRP C 59 HIS 0.007 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8336) covalent geometry : angle 0.68648 (11263) hydrogen bonds : bond 0.04050 ( 507) hydrogen bonds : angle 4.54330 ( 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 187 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.275 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 518 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6234 (tpm170) REVERT: B 94 MET cc_start: 0.7897 (pmm) cc_final: 0.7554 (pmm) REVERT: B 185 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7277 (tppt) REVERT: B 230 MET cc_start: 0.4417 (ttm) cc_final: 0.3595 (ttt) REVERT: C 15 GLN cc_start: 0.9380 (mt0) cc_final: 0.9050 (pt0) REVERT: D 14 GLU cc_start: 0.8863 (tt0) cc_final: 0.8533 (tp30) REVERT: D 22 MET cc_start: 0.7690 (ptm) cc_final: 0.6935 (ptp) REVERT: D 139 ASN cc_start: 0.9315 (m-40) cc_final: 0.9055 (t0) outliers start: 25 outliers final: 21 residues processed: 174 average time/residue: 0.0713 time to fit residues: 17.5799 Evaluate side-chains 179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 518 ARG Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS 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 C residue 212 LYS 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=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: 6.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.083595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070283 restraints weight = 34554.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072014 restraints weight = 21888.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073295 restraints weight = 15990.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074220 restraints weight = 12626.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074908 restraints weight = 10594.312| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8336 Z= 0.171 Angle : 0.708 13.773 11263 Z= 0.361 Chirality : 0.044 0.308 1246 Planarity : 0.004 0.048 1435 Dihedral : 9.015 154.412 1160 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.18 % Allowed : 22.25 % Favored : 74.57 % 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: 0.45 (0.26), residues: 1007 helix: 1.28 (0.20), residues: 607 sheet: -0.98 (0.62), residues: 57 loop : -1.22 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 167 TYR 0.041 0.002 TYR C 211 PHE 0.020 0.002 PHE A 559 TRP 0.019 0.002 TRP C 59 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8336) covalent geometry : angle 0.70755 (11263) hydrogen bonds : bond 0.04119 ( 507) hydrogen bonds : angle 4.66880 ( 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 188 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.278 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 518 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6361 (tpm170) REVERT: A 560 MET cc_start: 0.8880 (mmt) cc_final: 0.8105 (mmm) REVERT: B 94 MET cc_start: 0.7876 (pmm) cc_final: 0.7526 (pmm) REVERT: B 230 MET cc_start: 0.4452 (ttm) cc_final: 0.3650 (ttt) REVERT: C 15 GLN cc_start: 0.9394 (mt0) cc_final: 0.9075 (pt0) REVERT: C 21 ASP cc_start: 0.7953 (t0) cc_final: 0.7711 (t0) REVERT: D 14 GLU cc_start: 0.8910 (tt0) cc_final: 0.8652 (tp30) REVERT: D 22 MET cc_start: 0.7686 (ptm) cc_final: 0.7193 (ptm) REVERT: D 139 ASN cc_start: 0.9280 (m-40) cc_final: 0.8989 (t0) REVERT: D 155 ILE cc_start: 0.9502 (mt) cc_final: 0.9258 (tt) outliers start: 28 outliers final: 25 residues processed: 173 average time/residue: 0.0719 time to fit residues: 17.8220 Evaluate side-chains 179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 477 HIS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 555 ASP 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 123 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.082997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.070181 restraints weight = 34101.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071861 restraints weight = 22093.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072781 restraints weight = 16231.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.073833 restraints weight = 13475.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074544 restraints weight = 11242.545| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5481 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= 0.141 Angle : 0.751 14.593 11263 Z= 0.372 Chirality : 0.044 0.301 1246 Planarity : 0.004 0.060 1435 Dihedral : 9.024 154.618 1160 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.61 % Allowed : 23.61 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1007 helix: 1.34 (0.20), residues: 606 sheet: -1.00 (0.62), residues: 56 loop : -1.20 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 167 TYR 0.019 0.001 TYR C 211 PHE 0.018 0.002 PHE A 559 TRP 0.010 0.001 TRP B 247 HIS 0.007 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8336) covalent geometry : angle 0.75141 (11263) hydrogen bonds : bond 0.04004 ( 507) hydrogen bonds : angle 4.62972 ( 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 184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.326 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: A 518 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.6236 (tpm170) REVERT: A 560 MET cc_start: 0.8920 (mmt) cc_final: 0.8151 (mmm) REVERT: B 94 MET cc_start: 0.7873 (pmm) cc_final: 0.7553 (pmm) REVERT: B 185 LYS cc_start: 0.7897 (tptt) cc_final: 0.7345 (tppt) REVERT: B 230 MET cc_start: 0.4255 (ttm) cc_final: 0.3432 (ttt) REVERT: C 219 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8830 (tp-100) REVERT: D 14 GLU cc_start: 0.8862 (tt0) cc_final: 0.8623 (tp30) REVERT: D 22 MET cc_start: 0.7678 (ptm) cc_final: 0.7278 (ptm) REVERT: D 139 ASN cc_start: 0.9311 (m-40) cc_final: 0.9027 (t0) outliers start: 23 outliers final: 19 residues processed: 173 average time/residue: 0.0655 time to fit residues: 16.4066 Evaluate side-chains 172 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 518 ARG 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.083309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.070279 restraints weight = 34038.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.071968 restraints weight = 21792.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073220 restraints weight = 16014.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074151 restraints weight = 12798.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074602 restraints weight = 10675.471| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8336 Z= 0.146 Angle : 0.758 14.589 11263 Z= 0.381 Chirality : 0.045 0.298 1246 Planarity : 0.004 0.057 1435 Dihedral : 9.038 152.733 1160 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.61 % Allowed : 23.95 % Favored : 73.44 % 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: 0.42 (0.26), residues: 1007 helix: 1.23 (0.20), residues: 608 sheet: -0.85 (0.62), residues: 56 loop : -1.22 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 167 TYR 0.045 0.001 TYR C 211 PHE 0.019 0.002 PHE A 559 TRP 0.011 0.001 TRP B 247 HIS 0.009 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8336) covalent geometry : angle 0.75835 (11263) hydrogen bonds : bond 0.04047 ( 507) hydrogen bonds : angle 4.74869 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.75 seconds wall clock time: 25 minutes 33.81 seconds (1533.81 seconds total)