Starting phenix.real_space_refine on Tue Mar 3 18:56:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jz3_22529/03_2026/7jz3_22529_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jz3_22529/03_2026/7jz3_22529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2026/7jz3_22529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2026/7jz3_22529.map" model { file = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2026/7jz3_22529_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jz3_22529/03_2026/7jz3_22529_neut.cif" } resolution = 2.56 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 ------------------------------------------------------------------------------- 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= 0.212 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 5097 2.51 5 N 1374 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8142 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Restraints were copied for chains: C, A Time building chain proxies: 1.90, per 1000 atoms: 0.23 Number of scatterers: 8142 At special positions: 0 Unit cell: (93.96, 92.88, 71.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 1662 8.00 N 1374 7.00 C 5097 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: 0.68 Conformation dependent library (CDL) restraints added in 358.8 milliseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 3 sheets defined 6.4% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 4 through 5 current: chain 'B' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL B 75 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 59 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B 73 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 61 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER B 71 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 91 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN B 93 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN B 126 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG B 217 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA B 244 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN B 254 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 245 " --> pdb=" O TRP B 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP B 252 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 255 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 283 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 281 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 279 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY B 282 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 293 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 4 through 5 current: chain 'C' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL C 75 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C 59 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR C 73 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN C 61 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER C 71 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 91 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN C 93 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN C 126 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG C 217 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 244 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C 254 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR C 245 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP C 252 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 255 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 283 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 281 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 279 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY C 282 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP C 293 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 5 current: chain 'A' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL A 75 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 59 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 73 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN A 61 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 71 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 91 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 93 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN A 126 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG A 217 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 244 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN A 254 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 245 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP A 252 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 255 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 283 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 281 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 279 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 265 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY A 282 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP A 293 " --> pdb=" O GLY A 282 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1089 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: 1.31 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2154 1.33 - 1.45: 1915 1.45 - 1.57: 4232 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 8319 Sorted by residual: bond pdb=" CA ASN C 133 " pdb=" CB ASN C 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.37e+00 bond pdb=" CA ASN B 133 " pdb=" CB ASN B 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.26e+00 bond pdb=" CA ASN A 133 " pdb=" CB ASN A 133 " ideal model delta sigma weight residual 1.530 1.492 0.039 1.55e-02 4.16e+03 6.21e+00 bond pdb=" N ASN C 133 " pdb=" CA ASN C 133 " ideal model delta sigma weight residual 1.455 1.427 0.028 1.22e-02 6.72e+03 5.39e+00 bond pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta sigma weight residual 1.455 1.428 0.028 1.22e-02 6.72e+03 5.11e+00 ... (remaining 8314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 10773 1.39 - 2.79: 428 2.79 - 4.18: 53 4.18 - 5.57: 8 5.57 - 6.97: 3 Bond angle restraints: 11265 Sorted by residual: angle pdb=" N VAL B 29 " pdb=" CA VAL B 29 " pdb=" C VAL B 29 " ideal model delta sigma weight residual 113.53 109.81 3.72 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N VAL C 29 " pdb=" CA VAL C 29 " pdb=" C VAL C 29 " ideal model delta sigma weight residual 113.53 109.83 3.70 9.80e-01 1.04e+00 1.42e+01 angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 113.53 109.85 3.68 9.80e-01 1.04e+00 1.41e+01 angle pdb=" N GLY C 138 " pdb=" CA GLY C 138 " pdb=" C GLY C 138 " ideal model delta sigma weight residual 115.32 119.34 -4.02 1.38e+00 5.25e-01 8.49e+00 angle pdb=" N GLY B 138 " pdb=" CA GLY B 138 " pdb=" C GLY B 138 " ideal model delta sigma weight residual 115.32 119.33 -4.01 1.38e+00 5.25e-01 8.43e+00 ... (remaining 11260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 4233 16.34 - 32.69: 365 32.69 - 49.03: 88 49.03 - 65.37: 15 65.37 - 81.71: 6 Dihedral angle restraints: 4707 sinusoidal: 1791 harmonic: 2916 Sorted by residual: dihedral pdb=" CA GLN A 237 " pdb=" CB GLN A 237 " pdb=" CG GLN A 237 " pdb=" CD GLN A 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.89 50.89 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " pdb=" CG GLN B 237 " pdb=" CD GLN B 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.88 50.88 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN C 237 " pdb=" CB GLN C 237 " pdb=" CG GLN C 237 " pdb=" CD GLN C 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.86 50.86 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 4704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 722 0.037 - 0.073: 279 0.073 - 0.110: 91 0.110 - 0.147: 30 0.147 - 0.183: 6 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA PHE C 136 " pdb=" N PHE C 136 " pdb=" C PHE C 136 " pdb=" CB PHE C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PHE B 136 " pdb=" N PHE B 136 " pdb=" C PHE B 136 " pdb=" CB PHE B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA PHE A 136 " pdb=" N PHE A 136 " pdb=" C PHE A 136 " pdb=" CB PHE A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1125 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 84 " -0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CG ASP A 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 84 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" CG ASP C 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP C 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 84 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" CG ASP B 84 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP B 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 838 2.75 - 3.29: 7936 3.29 - 3.82: 13672 3.82 - 4.36: 17117 4.36 - 4.90: 30181 Nonbonded interactions: 69744 Sorted by model distance: nonbonded pdb=" NE2 GLN B 237 " pdb=" OG1 THR B 239 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN C 237 " pdb=" OG1 THR C 239 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN A 237 " pdb=" OG1 THR A 239 " model vdw 2.211 3.120 nonbonded pdb=" OD2 ASP A 89 " pdb=" ND2 ASN A 93 " model vdw 2.288 3.120 nonbonded pdb=" OD2 ASP B 89 " pdb=" ND2 ASN B 93 " model vdw 2.289 3.120 ... (remaining 69739 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8319 Z= 0.195 Angle : 0.623 6.968 11265 Z= 0.384 Chirality : 0.046 0.183 1128 Planarity : 0.003 0.038 1530 Dihedral : 13.643 81.714 2913 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.09 % Allowed : 7.27 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.23), residues: 1032 helix: -2.59 (0.66), residues: 42 sheet: -0.80 (0.20), residues: 561 loop : -2.78 (0.24), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 202 TYR 0.012 0.001 TYR B 58 PHE 0.011 0.002 PHE B 269 TRP 0.005 0.001 TRP A 56 HIS 0.002 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8319) covalent geometry : angle 0.62312 (11265) hydrogen bonds : bond 0.13421 ( 384) hydrogen bonds : angle 6.61973 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 281 LYS cc_start: 0.5712 (mttm) cc_final: 0.5058 (mptt) REVERT: B 291 ASP cc_start: 0.5276 (m-30) cc_final: 0.4920 (t0) REVERT: C 281 LYS cc_start: 0.5715 (mttm) cc_final: 0.5460 (mttm) REVERT: C 310 MET cc_start: 0.7723 (tpt) cc_final: 0.7399 (tpt) REVERT: A 281 LYS cc_start: 0.5722 (mttm) cc_final: 0.5054 (mptt) REVERT: A 291 ASP cc_start: 0.5276 (m-30) cc_final: 0.4989 (t0) REVERT: A 319 ASN cc_start: 0.5859 (t0) cc_final: 0.5251 (t0) outliers start: 9 outliers final: 5 residues processed: 203 average time/residue: 0.4095 time to fit residues: 89.6707 Evaluate side-chains 156 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 21 HIS B 45 GLN B 61 GLN B 83 GLN B 144 ASN B 231 ASN B 264 GLN C 45 GLN C 61 GLN C 69 ASN C 144 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN A 9 ASN A 21 HIS A 45 GLN A 61 GLN A 144 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 264 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.252270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.240639 restraints weight = 9786.264| |-----------------------------------------------------------------------------| r_work (start): 0.4744 rms_B_bonded: 1.80 r_work: 0.4698 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4607 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8319 Z= 0.282 Angle : 0.828 10.610 11265 Z= 0.444 Chirality : 0.052 0.156 1128 Planarity : 0.005 0.041 1530 Dihedral : 6.114 58.546 1171 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.85 % Allowed : 18.55 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.23), residues: 1032 helix: -2.51 (0.55), residues: 60 sheet: -0.61 (0.20), residues: 543 loop : -3.13 (0.23), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 170 TYR 0.023 0.003 TYR C 313 PHE 0.035 0.003 PHE C 40 TRP 0.011 0.002 TRP A 252 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00628 ( 8319) covalent geometry : angle 0.82849 (11265) hydrogen bonds : bond 0.04380 ( 384) hydrogen bonds : angle 6.35630 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.285 Fit side-chains REVERT: B 120 PHE cc_start: 0.6165 (m-80) cc_final: 0.5950 (m-80) REVERT: B 178 ASP cc_start: 0.6880 (m-30) cc_final: 0.6592 (m-30) REVERT: B 189 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6832 (tm-30) REVERT: B 281 LYS cc_start: 0.5231 (mttm) cc_final: 0.4276 (mttp) REVERT: B 319 ASN cc_start: 0.6967 (t0) cc_final: 0.6512 (t0) REVERT: C 27 LYS cc_start: 0.7524 (mptt) cc_final: 0.6733 (mptm) REVERT: C 83 GLN cc_start: 0.7982 (pt0) cc_final: 0.7739 (pt0) REVERT: C 189 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6857 (tm-30) REVERT: C 219 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.3890 (mp0) REVERT: C 281 LYS cc_start: 0.5449 (mttm) cc_final: 0.4570 (mttp) REVERT: C 310 MET cc_start: 0.7887 (tpt) cc_final: 0.7609 (tpt) REVERT: A 73 THR cc_start: 0.7642 (p) cc_final: 0.7346 (p) REVERT: A 189 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6865 (tm-30) REVERT: A 281 LYS cc_start: 0.5572 (mttm) cc_final: 0.4417 (mptt) REVERT: A 287 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7156 (mtp85) outliers start: 40 outliers final: 18 residues processed: 198 average time/residue: 0.4252 time to fit residues: 90.4417 Evaluate side-chains 179 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 304 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 144 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.252171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.240774 restraints weight = 9702.012| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 1.79 r_work: 0.4702 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4615 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8319 Z= 0.254 Angle : 0.796 9.532 11265 Z= 0.428 Chirality : 0.051 0.186 1128 Planarity : 0.005 0.038 1530 Dihedral : 5.943 49.039 1169 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 6.18 % Allowed : 21.94 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.23), residues: 1032 helix: -2.06 (0.61), residues: 60 sheet: -0.60 (0.21), residues: 543 loop : -3.15 (0.24), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 170 TYR 0.022 0.003 TYR C 313 PHE 0.027 0.003 PHE C 40 TRP 0.010 0.002 TRP A 56 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 8319) covalent geometry : angle 0.79565 (11265) hydrogen bonds : bond 0.03954 ( 384) hydrogen bonds : angle 6.38247 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.277 Fit side-chains REVERT: B 57 GLU cc_start: 0.7797 (tt0) cc_final: 0.7387 (tt0) REVERT: B 178 ASP cc_start: 0.6910 (m-30) cc_final: 0.6663 (m-30) REVERT: B 252 TRP cc_start: 0.6794 (OUTLIER) cc_final: 0.5506 (m-90) REVERT: B 281 LYS cc_start: 0.5273 (mttm) cc_final: 0.4189 (mttt) REVERT: C 27 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6821 (mmtp) REVERT: C 83 GLN cc_start: 0.7944 (pt0) cc_final: 0.7736 (pt0) REVERT: C 126 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6962 (m110) REVERT: C 189 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6740 (tm-30) REVERT: C 219 GLU cc_start: 0.4889 (OUTLIER) cc_final: 0.3886 (mp0) REVERT: C 258 ASN cc_start: 0.7104 (OUTLIER) cc_final: 0.6712 (m-40) REVERT: C 281 LYS cc_start: 0.5495 (mttm) cc_final: 0.4442 (mttt) REVERT: C 287 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6914 (mtt180) REVERT: A 73 THR cc_start: 0.7631 (p) cc_final: 0.7331 (p) REVERT: A 122 GLN cc_start: 0.4634 (OUTLIER) cc_final: 0.4398 (mt0) REVERT: A 189 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6659 (tm-30) REVERT: A 281 LYS cc_start: 0.5641 (mttm) cc_final: 0.4518 (mttt) outliers start: 51 outliers final: 26 residues processed: 207 average time/residue: 0.4002 time to fit residues: 89.2696 Evaluate side-chains 196 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 304 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 126 ASN B 264 GLN C 9 ASN C 126 ASN C 144 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.252247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.240771 restraints weight = 9793.888| |-----------------------------------------------------------------------------| r_work (start): 0.4742 rms_B_bonded: 1.78 r_work: 0.4698 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4610 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8319 Z= 0.244 Angle : 0.784 9.832 11265 Z= 0.420 Chirality : 0.050 0.214 1128 Planarity : 0.005 0.038 1530 Dihedral : 5.932 41.641 1168 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 8.12 % Allowed : 22.55 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.24), residues: 1032 helix: -2.38 (0.58), residues: 60 sheet: -0.55 (0.21), residues: 543 loop : -3.17 (0.24), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 170 TYR 0.022 0.003 TYR C 98 PHE 0.023 0.003 PHE C 40 TRP 0.010 0.002 TRP C 252 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 8319) covalent geometry : angle 0.78377 (11265) hydrogen bonds : bond 0.03825 ( 384) hydrogen bonds : angle 6.40254 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.7836 (tt0) cc_final: 0.7402 (tt0) REVERT: B 178 ASP cc_start: 0.6919 (m-30) cc_final: 0.6647 (m-30) REVERT: B 189 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7139 (tm-30) REVERT: B 252 TRP cc_start: 0.6831 (OUTLIER) cc_final: 0.5427 (m-90) REVERT: B 281 LYS cc_start: 0.5300 (mttm) cc_final: 0.4210 (mttt) REVERT: C 27 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6794 (mmtp) REVERT: C 57 GLU cc_start: 0.7861 (tt0) cc_final: 0.7629 (tt0) REVERT: C 170 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5676 (ptp-170) REVERT: C 189 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6808 (tm-30) REVERT: C 219 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.3921 (mp0) REVERT: C 258 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6730 (m-40) REVERT: C 281 LYS cc_start: 0.5524 (mttm) cc_final: 0.4501 (mttt) REVERT: A 189 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6588 (tm-30) REVERT: A 227 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.3997 (t80) REVERT: A 281 LYS cc_start: 0.5638 (mttm) cc_final: 0.4659 (mttp) outliers start: 67 outliers final: 37 residues processed: 211 average time/residue: 0.4269 time to fit residues: 97.0058 Evaluate side-chains 204 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 264 GLN C 21 HIS C 126 ASN C 144 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN A 144 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.250611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.239362 restraints weight = 9783.525| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 1.74 r_work: 0.4687 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4601 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8319 Z= 0.272 Angle : 0.821 9.952 11265 Z= 0.441 Chirality : 0.051 0.204 1128 Planarity : 0.005 0.038 1530 Dihedral : 6.083 42.203 1168 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 8.73 % Allowed : 24.00 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.24), residues: 1032 helix: -2.60 (0.57), residues: 60 sheet: -0.62 (0.21), residues: 546 loop : -3.24 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 170 TYR 0.023 0.003 TYR C 98 PHE 0.026 0.003 PHE B 120 TRP 0.011 0.002 TRP C 252 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 8319) covalent geometry : angle 0.82130 (11265) hydrogen bonds : bond 0.04026 ( 384) hydrogen bonds : angle 6.52052 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 0.202 Fit side-chains REVERT: B 57 GLU cc_start: 0.7830 (tt0) cc_final: 0.7415 (tt0) REVERT: B 178 ASP cc_start: 0.6922 (m-30) cc_final: 0.6679 (m-30) REVERT: B 189 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7021 (tm-30) REVERT: B 252 TRP cc_start: 0.6851 (OUTLIER) cc_final: 0.5442 (m-90) REVERT: B 281 LYS cc_start: 0.5390 (mttm) cc_final: 0.4253 (mptt) REVERT: C 27 LYS cc_start: 0.7608 (mptt) cc_final: 0.6644 (mmtt) REVERT: C 126 ASN cc_start: 0.7127 (OUTLIER) cc_final: 0.6708 (m-40) REVERT: C 170 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5522 (ptp-170) REVERT: C 189 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6863 (tm-30) REVERT: C 219 GLU cc_start: 0.4921 (OUTLIER) cc_final: 0.3902 (mp0) REVERT: C 258 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6737 (m-40) REVERT: C 281 LYS cc_start: 0.5570 (mttm) cc_final: 0.4588 (mttt) REVERT: C 294 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6625 (mm) REVERT: A 83 GLN cc_start: 0.7771 (pt0) cc_final: 0.7463 (pt0) REVERT: A 252 TRP cc_start: 0.6978 (OUTLIER) cc_final: 0.5224 (m-90) REVERT: A 281 LYS cc_start: 0.5757 (mttm) cc_final: 0.4642 (mttt) outliers start: 72 outliers final: 43 residues processed: 218 average time/residue: 0.3972 time to fit residues: 93.3304 Evaluate side-chains 212 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 83 GLN C 126 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.252790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.241520 restraints weight = 9658.870| |-----------------------------------------------------------------------------| r_work (start): 0.4740 rms_B_bonded: 1.77 r_work: 0.4697 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4610 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8319 Z= 0.221 Angle : 0.766 9.767 11265 Z= 0.409 Chirality : 0.049 0.165 1128 Planarity : 0.005 0.054 1530 Dihedral : 5.900 38.868 1168 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 8.36 % Allowed : 25.82 % Favored : 65.82 % 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: -2.40 (0.24), residues: 1032 helix: -1.82 (0.78), residues: 42 sheet: -0.53 (0.21), residues: 546 loop : -2.98 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 174 TYR 0.027 0.003 TYR C 98 PHE 0.020 0.002 PHE C 40 TRP 0.010 0.002 TRP C 252 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8319) covalent geometry : angle 0.76624 (11265) hydrogen bonds : bond 0.03692 ( 384) hydrogen bonds : angle 6.33929 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 168 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.7790 (tt0) cc_final: 0.7386 (tt0) REVERT: B 178 ASP cc_start: 0.6953 (m-30) cc_final: 0.6681 (m-30) REVERT: B 189 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 281 LYS cc_start: 0.5358 (mttm) cc_final: 0.4238 (mttt) REVERT: C 27 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.6825 (mmtp) REVERT: C 57 GLU cc_start: 0.7883 (tt0) cc_final: 0.7669 (tt0) REVERT: C 73 THR cc_start: 0.7656 (t) cc_final: 0.7344 (m) REVERT: C 92 ARG cc_start: 0.6109 (ttt180) cc_final: 0.5868 (tpt170) REVERT: C 189 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6780 (tm-30) REVERT: C 219 GLU cc_start: 0.4884 (OUTLIER) cc_final: 0.3889 (mp0) REVERT: C 258 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6775 (m-40) REVERT: C 281 LYS cc_start: 0.5506 (mttm) cc_final: 0.4523 (mttt) REVERT: A 189 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6608 (tm-30) REVERT: A 252 TRP cc_start: 0.6849 (OUTLIER) cc_final: 0.5138 (m-90) REVERT: A 255 LYS cc_start: 0.5976 (mttt) cc_final: 0.5651 (mttp) REVERT: A 281 LYS cc_start: 0.5729 (mttm) cc_final: 0.4602 (mttt) outliers start: 69 outliers final: 48 residues processed: 215 average time/residue: 0.4027 time to fit residues: 93.3715 Evaluate side-chains 213 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 83 GLN C 126 ASN C 153 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.251678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.239955 restraints weight = 9822.637| |-----------------------------------------------------------------------------| r_work (start): 0.4740 rms_B_bonded: 1.81 r_work: 0.4695 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4607 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8319 Z= 0.233 Angle : 0.785 9.895 11265 Z= 0.420 Chirality : 0.050 0.189 1128 Planarity : 0.005 0.062 1530 Dihedral : 5.935 39.109 1168 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 9.33 % Allowed : 26.79 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.24), residues: 1032 helix: -1.81 (0.78), residues: 42 sheet: -0.45 (0.22), residues: 543 loop : -3.00 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 174 TYR 0.031 0.003 TYR A 98 PHE 0.019 0.002 PHE C 40 TRP 0.013 0.002 TRP C 252 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 8319) covalent geometry : angle 0.78504 (11265) hydrogen bonds : bond 0.03746 ( 384) hydrogen bonds : angle 6.36318 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.7791 (tt0) cc_final: 0.7350 (tt0) REVERT: B 178 ASP cc_start: 0.6969 (m-30) cc_final: 0.6679 (m-30) REVERT: B 189 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 281 LYS cc_start: 0.5334 (mttm) cc_final: 0.4226 (mptt) REVERT: C 27 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6621 (mmtt) REVERT: C 73 THR cc_start: 0.7496 (t) cc_final: 0.7187 (m) REVERT: C 189 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6743 (tm-30) REVERT: C 217 ARG cc_start: 0.6109 (mtp180) cc_final: 0.5812 (ptm160) REVERT: C 219 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.3908 (mp0) REVERT: C 258 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6776 (m-40) REVERT: C 281 LYS cc_start: 0.5589 (mttm) cc_final: 0.4607 (mttt) REVERT: C 294 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6572 (mm) REVERT: A 83 GLN cc_start: 0.7783 (pt0) cc_final: 0.7492 (pt0) REVERT: A 189 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6466 (tm-30) REVERT: A 219 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.3955 (mp0) REVERT: A 227 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.3773 (t80) REVERT: A 252 TRP cc_start: 0.6851 (OUTLIER) cc_final: 0.5120 (m-90) REVERT: A 255 LYS cc_start: 0.5926 (mttt) cc_final: 0.5600 (mttp) REVERT: A 281 LYS cc_start: 0.5695 (mttm) cc_final: 0.4539 (mttt) outliers start: 77 outliers final: 55 residues processed: 219 average time/residue: 0.3779 time to fit residues: 90.0094 Evaluate side-chains 218 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 156 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 148 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 126 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.252697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.241072 restraints weight = 9645.853| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 1.81 r_work: 0.4706 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4618 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8319 Z= 0.217 Angle : 0.772 9.892 11265 Z= 0.413 Chirality : 0.049 0.169 1128 Planarity : 0.005 0.055 1530 Dihedral : 5.851 38.006 1168 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 8.48 % Allowed : 27.76 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.24), residues: 1032 helix: -1.80 (0.78), residues: 42 sheet: -0.43 (0.22), residues: 546 loop : -2.91 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 174 TYR 0.034 0.003 TYR A 98 PHE 0.018 0.002 PHE C 40 TRP 0.013 0.002 TRP C 252 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8319) covalent geometry : angle 0.77196 (11265) hydrogen bonds : bond 0.03664 ( 384) hydrogen bonds : angle 6.28526 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 165 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.7785 (tt0) cc_final: 0.7331 (tt0) REVERT: B 178 ASP cc_start: 0.6938 (m-30) cc_final: 0.6628 (m-30) REVERT: B 189 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6992 (tm-30) REVERT: B 281 LYS cc_start: 0.5240 (mttm) cc_final: 0.4116 (mptt) REVERT: C 27 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.6607 (mmtt) REVERT: C 49 GLN cc_start: 0.6870 (mt0) cc_final: 0.6493 (mm-40) REVERT: C 73 THR cc_start: 0.7476 (t) cc_final: 0.7124 (m) REVERT: C 120 PHE cc_start: 0.6172 (m-80) cc_final: 0.5804 (m-80) REVERT: C 170 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.5249 (ptp-110) REVERT: C 189 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6776 (tm-30) REVERT: C 219 GLU cc_start: 0.4956 (OUTLIER) cc_final: 0.3971 (mp0) REVERT: C 258 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6805 (m-40) REVERT: C 281 LYS cc_start: 0.5547 (mttm) cc_final: 0.4662 (mtmm) REVERT: C 294 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6629 (mm) REVERT: A 189 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6480 (tm-30) REVERT: A 219 GLU cc_start: 0.5433 (OUTLIER) cc_final: 0.3944 (mp0) REVERT: A 252 TRP cc_start: 0.6789 (OUTLIER) cc_final: 0.5083 (m-90) REVERT: A 255 LYS cc_start: 0.5908 (mttt) cc_final: 0.5580 (mttp) REVERT: A 281 LYS cc_start: 0.5736 (mttm) cc_final: 0.4538 (mttt) outliers start: 70 outliers final: 54 residues processed: 214 average time/residue: 0.4130 time to fit residues: 95.4543 Evaluate side-chains 219 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 158 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 126 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.255489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.244370 restraints weight = 9655.353| |-----------------------------------------------------------------------------| r_work (start): 0.4769 rms_B_bonded: 1.76 r_work: 0.4726 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4639 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8319 Z= 0.177 Angle : 0.730 9.579 11265 Z= 0.390 Chirality : 0.048 0.146 1128 Planarity : 0.004 0.055 1530 Dihedral : 5.539 32.808 1168 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 7.52 % Allowed : 28.36 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.25), residues: 1032 helix: -1.85 (0.75), residues: 42 sheet: -0.34 (0.22), residues: 546 loop : -2.76 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 174 TYR 0.032 0.002 TYR B 98 PHE 0.017 0.002 PHE C 40 TRP 0.011 0.002 TRP C 252 HIS 0.002 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8319) covalent geometry : angle 0.73000 (11265) hydrogen bonds : bond 0.03384 ( 384) hydrogen bonds : angle 6.08742 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.235 Fit side-chains REVERT: B 178 ASP cc_start: 0.6880 (m-30) cc_final: 0.6610 (m-30) REVERT: B 189 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 281 LYS cc_start: 0.5211 (mttm) cc_final: 0.4065 (mptt) REVERT: C 27 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6585 (mmtt) REVERT: C 73 THR cc_start: 0.7375 (t) cc_final: 0.6995 (m) REVERT: C 83 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: C 92 ARG cc_start: 0.5937 (ttt180) cc_final: 0.5688 (tpt170) REVERT: C 120 PHE cc_start: 0.6133 (m-80) cc_final: 0.5841 (m-80) REVERT: C 170 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.5272 (ptp-170) REVERT: C 189 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6666 (tm-30) REVERT: C 219 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.3965 (mp0) REVERT: C 258 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6914 (m110) REVERT: C 281 LYS cc_start: 0.5458 (mttm) cc_final: 0.4447 (mptt) REVERT: A 12 ASP cc_start: 0.6089 (p0) cc_final: 0.5770 (p0) REVERT: A 189 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6585 (tm-30) REVERT: A 219 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.3926 (mp0) REVERT: A 252 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5096 (m-90) REVERT: A 281 LYS cc_start: 0.5706 (mttm) cc_final: 0.4572 (mttt) outliers start: 62 outliers final: 46 residues processed: 209 average time/residue: 0.3893 time to fit residues: 88.0285 Evaluate side-chains 206 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 150 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 150 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.251435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.239855 restraints weight = 9700.892| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 1.80 r_work: 0.4698 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4609 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8319 Z= 0.257 Angle : 0.821 10.106 11265 Z= 0.441 Chirality : 0.050 0.183 1128 Planarity : 0.005 0.055 1530 Dihedral : 5.893 33.410 1168 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 7.64 % Allowed : 28.85 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.25), residues: 1032 helix: -1.76 (0.79), residues: 42 sheet: -0.41 (0.22), residues: 543 loop : -2.84 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 174 TYR 0.042 0.003 TYR C 98 PHE 0.035 0.003 PHE A 40 TRP 0.021 0.002 TRP C 252 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 8319) covalent geometry : angle 0.82121 (11265) hydrogen bonds : bond 0.03939 ( 384) hydrogen bonds : angle 6.36804 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 161 time to evaluate : 0.280 Fit side-chains REVERT: B 57 GLU cc_start: 0.7978 (tt0) cc_final: 0.7611 (tp30) REVERT: B 178 ASP cc_start: 0.6967 (m-30) cc_final: 0.6706 (m-30) REVERT: B 189 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6909 (tm-30) REVERT: B 281 LYS cc_start: 0.5295 (mttm) cc_final: 0.4205 (mptt) REVERT: C 27 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.6624 (mmtt) REVERT: C 73 THR cc_start: 0.7472 (t) cc_final: 0.7116 (m) REVERT: C 83 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: C 170 ARG cc_start: 0.5692 (OUTLIER) cc_final: 0.5313 (ptp-110) REVERT: C 189 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6661 (tm-30) REVERT: C 219 GLU cc_start: 0.4969 (OUTLIER) cc_final: 0.3942 (mp0) REVERT: C 281 LYS cc_start: 0.5602 (mttm) cc_final: 0.4609 (mttt) REVERT: A 12 ASP cc_start: 0.6214 (p0) cc_final: 0.5894 (p0) REVERT: A 189 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6510 (tm-30) REVERT: A 219 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.3925 (mp0) REVERT: A 252 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.5125 (m-90) REVERT: A 255 LYS cc_start: 0.5868 (mttt) cc_final: 0.5525 (mttp) REVERT: A 281 LYS cc_start: 0.5754 (mttm) cc_final: 0.4595 (mttt) outliers start: 63 outliers final: 50 residues processed: 205 average time/residue: 0.3791 time to fit residues: 84.5364 Evaluate side-chains 210 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.250932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.239376 restraints weight = 9743.480| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 1.80 r_work: 0.4695 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4606 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8319 Z= 0.273 Angle : 0.853 10.146 11265 Z= 0.457 Chirality : 0.051 0.189 1128 Planarity : 0.006 0.061 1530 Dihedral : 5.915 33.899 1166 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 7.52 % Allowed : 29.33 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.25), residues: 1032 helix: -1.87 (0.77), residues: 42 sheet: -0.42 (0.22), residues: 540 loop : -2.95 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 174 TYR 0.051 0.003 TYR A 98 PHE 0.036 0.003 PHE A 40 TRP 0.018 0.002 TRP C 252 HIS 0.003 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 8319) covalent geometry : angle 0.85256 (11265) hydrogen bonds : bond 0.04121 ( 384) hydrogen bonds : angle 6.42890 ( 1089) =============================================================================== Job complete usr+sys time: 2792.86 seconds wall clock time: 48 minutes 22.67 seconds (2902.67 seconds total)