Starting phenix.real_space_refine on Tue Aug 4 16:55:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9swm_55320/08_2026/9swm_55320.cif Found real_map, /net/cci-nas-00/data/ceres_data/9swm_55320/08_2026/9swm_55320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9swm_55320/08_2026/9swm_55320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9swm_55320/08_2026/9swm_55320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9swm_55320/08_2026/9swm_55320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9swm_55320/08_2026/9swm_55320.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 24 5.16 5 C 3204 2.51 5 N 870 2.21 5 O 904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5002 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2500 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2502 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 1.16, per 1000 atoms: 0.23 Number of scatterers: 5002 At special positions: 0 Unit cell: (60.852, 92.661, 112.023, 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 24 16.00 O 904 8.00 N 870 7.00 C 3204 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: 0.25 Conformation dependent library (CDL) restraints added in 115.1 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 2 sheets defined 60.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.657A pdb=" N LYS A 20 " --> pdb=" O HIS A 16 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 70 removed outlier: 3.892A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.625A pdb=" N VAL A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.930A pdb=" N ARG A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 116 through 134 removed outlier: 4.246A pdb=" N MET A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.639A pdb=" N TYR A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 184 through 190 removed outlier: 4.407A pdb=" N ASN A 187 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN A 188 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 190 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.112A pdb=" N ALA A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 211 through 216' Processing helix chain 'A' and resid 263 through 273 removed outlier: 4.015A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.832A pdb=" N HIS A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 33 removed outlier: 3.731A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 70 removed outlier: 4.133A pdb=" N LEU B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.686A pdb=" N TYR B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.777A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.801A pdb=" N ALA B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 134 removed outlier: 4.304A pdb=" N MET B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 156 through 167 removed outlier: 3.577A pdb=" N TYR B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Proline residue: B 173 - end of helix removed outlier: 4.283A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 4.929A pdb=" N ASN B 187 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 188 " --> pdb=" O HIS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.669A pdb=" N MET B 214 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 removed outlier: 4.048A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.720A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.744A pdb=" N HIS B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 224 removed outlier: 3.631A pdb=" N LEU A 222 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER A 243 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 258 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N TYR A 245 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 256 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 247 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 314 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 225 removed outlier: 5.873A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 248 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE B 221 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 246 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 223 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 244 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN B 242 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER B 243 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 259 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 199 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 260 " --> pdb=" O TYR B 199 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 726 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: 0.56 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1592 1.34 - 1.46: 747 1.46 - 1.57: 2749 1.57 - 1.69: 1 1.69 - 1.81: 28 Bond restraints: 5117 Sorted by residual: bond pdb=" C LEU A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.332 1.396 -0.065 1.30e-02 5.92e+03 2.47e+01 bond pdb=" CA PRO A 115 " pdb=" C PRO A 115 " ideal model delta sigma weight residual 1.514 1.531 -0.017 5.50e-03 3.31e+04 9.59e+00 bond pdb=" CA HIS A 42 " pdb=" C HIS A 42 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.41e-02 5.03e+03 8.48e+00 bond pdb=" C LEU B 109 " pdb=" N PRO B 110 " ideal model delta sigma weight residual 1.334 1.384 -0.051 2.34e-02 1.83e+03 4.67e+00 bond pdb=" CB GLN B 184 " pdb=" CG GLN B 184 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.63e+00 ... (remaining 5112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 6737 2.44 - 4.87: 166 4.87 - 7.31: 46 7.31 - 9.74: 12 9.74 - 12.18: 8 Bond angle restraints: 6969 Sorted by residual: angle pdb=" N PRO A 115 " pdb=" CA PRO A 115 " pdb=" CB PRO A 115 " ideal model delta sigma weight residual 103.19 109.98 -6.79 5.60e-01 3.19e+00 1.47e+02 angle pdb=" CA GLN B 184 " pdb=" CB GLN B 184 " pdb=" CG GLN B 184 " ideal model delta sigma weight residual 114.10 124.65 -10.55 2.00e+00 2.50e-01 2.78e+01 angle pdb=" N GLU B 38 " pdb=" CA GLU B 38 " pdb=" C GLU B 38 " ideal model delta sigma weight residual 109.81 120.94 -11.13 2.21e+00 2.05e-01 2.54e+01 angle pdb=" CB GLN B 184 " pdb=" CG GLN B 184 " pdb=" CD GLN B 184 " ideal model delta sigma weight residual 112.60 120.81 -8.21 1.70e+00 3.46e-01 2.33e+01 angle pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" C LEU A 172 " ideal model delta sigma weight residual 113.16 119.86 -6.70 1.42e+00 4.96e-01 2.23e+01 ... (remaining 6964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 2600 16.86 - 33.71: 322 33.71 - 50.56: 115 50.56 - 67.42: 15 67.42 - 84.27: 7 Dihedral angle restraints: 3059 sinusoidal: 1187 harmonic: 1872 Sorted by residual: dihedral pdb=" CA SER B 108 " pdb=" C SER B 108 " pdb=" N LEU B 109 " pdb=" CA LEU B 109 " ideal model delta harmonic sigma weight residual 180.00 147.02 32.98 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N PRO A 40 " pdb=" CA PRO A 40 " ideal model delta harmonic sigma weight residual 180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 3056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 597 0.047 - 0.094: 135 0.094 - 0.141: 45 0.141 - 0.188: 8 0.188 - 0.235: 5 Chirality restraints: 790 Sorted by residual: chirality pdb=" CA GLU B 38 " pdb=" N GLU B 38 " pdb=" C GLU B 38 " pdb=" CB GLU B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 73 " pdb=" CA ILE A 73 " pdb=" CG1 ILE A 73 " pdb=" CG2 ILE A 73 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 787 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 114 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO B 115 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 301 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" CG ASP A 301 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP A 301 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 301 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 39 " -0.039 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO B 40 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " -0.032 5.00e-02 4.00e+02 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1638 2.85 - 3.36: 4253 3.36 - 3.87: 7647 3.87 - 4.39: 7657 4.39 - 4.90: 13962 Nonbonded interactions: 35157 Sorted by model distance: nonbonded pdb=" OG SER A 280 " pdb=" OD2 ASP A 283 " model vdw 2.335 3.040 nonbonded pdb=" NE2 GLN A 306 " pdb=" OD1 ASN A 307 " model vdw 2.382 3.120 nonbonded pdb=" NE2 GLN B 306 " pdb=" OD1 ASN B 307 " model vdw 2.390 3.120 nonbonded pdb=" OE1 GLU B 69 " pdb=" OH TYR B 77 " model vdw 2.407 3.040 nonbonded pdb=" OG SER B 280 " pdb=" OD2 ASP B 283 " model vdw 2.409 3.040 ... (remaining 35152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 4 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 336)) } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.750 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 5117 Z= 0.240 Angle : 1.067 12.180 6969 Z= 0.557 Chirality : 0.050 0.235 790 Planarity : 0.007 0.081 897 Dihedral : 17.093 84.273 1859 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 0.38 % Allowed : 25.05 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.31), residues: 634 helix: -0.73 (0.26), residues: 337 sheet: 1.65 (0.72), residues: 40 loop : -1.46 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 180 TYR 0.009 0.001 TYR A 314 PHE 0.021 0.001 PHE B 117 TRP 0.010 0.001 TRP B 161 HIS 0.009 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.24 ( 5117) covalent geometry : angle 1.06652 / 0.56 ( 6969) hydrogen bonds : bond 0.13486 / 9.01 ( 246) hydrogen bonds : angle 5.53293 / 3.97 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8621 (ptt) cc_final: 0.7809 (pmm) REVERT: A 216 ASP cc_start: 0.8246 (t0) cc_final: 0.8040 (t0) REVERT: A 295 LEU cc_start: 0.9238 (tp) cc_final: 0.9035 (tt) REVERT: A 301 ASP cc_start: 0.8252 (t0) cc_final: 0.7618 (t0) REVERT: B 48 VAL cc_start: 0.8420 (m) cc_final: 0.8138 (p) REVERT: B 120 MET cc_start: 0.7386 (ptm) cc_final: 0.6848 (ptm) REVERT: B 121 LEU cc_start: 0.8779 (tt) cc_final: 0.8499 (mm) REVERT: B 155 VAL cc_start: 0.8677 (t) cc_final: 0.8451 (t) REVERT: B 202 LEU cc_start: 0.9051 (mm) cc_final: 0.8792 (mp) REVERT: B 216 ASP cc_start: 0.8953 (t0) cc_final: 0.8673 (t0) outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.0562 time to fit residues: 10.7883 Evaluate side-chains 106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.091138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068060 restraints weight = 14023.409| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 5.42 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5117 Z= 0.132 Angle : 0.662 8.741 6969 Z= 0.323 Chirality : 0.042 0.190 790 Planarity : 0.005 0.062 897 Dihedral : 5.221 36.656 714 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 5.08 % Allowed : 24.11 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.34), residues: 634 helix: 0.77 (0.29), residues: 339 sheet: 1.87 (0.80), residues: 28 loop : -1.15 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.008 0.001 TYR B 77 PHE 0.013 0.001 PHE A 117 TRP 0.007 0.001 TRP B 119 HIS 0.003 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5117) covalent geometry : angle 0.66208 / 0.32 ( 6969) hydrogen bonds : bond 0.03496 / 2.45 ( 246) hydrogen bonds : angle 3.99832 / 2.86 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8840 (mm-40) REVERT: A 120 MET cc_start: 0.8900 (ptt) cc_final: 0.8388 (ptp) REVERT: A 155 VAL cc_start: 0.9091 (t) cc_final: 0.8812 (m) REVERT: A 169 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.8525 (ttp-110) REVERT: A 188 ASN cc_start: 0.9524 (m110) cc_final: 0.9174 (p0) REVERT: A 282 GLU cc_start: 0.8624 (mp0) cc_final: 0.8405 (tp30) REVERT: B 120 MET cc_start: 0.8171 (ptm) cc_final: 0.7665 (ptm) REVERT: B 206 CYS cc_start: 0.9508 (m) cc_final: 0.9185 (p) REVERT: B 216 ASP cc_start: 0.8940 (t0) cc_final: 0.8314 (t0) outliers start: 27 outliers final: 17 residues processed: 122 average time/residue: 0.0478 time to fit residues: 8.3406 Evaluate side-chains 110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 292 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.090740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068008 restraints weight = 13841.118| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 5.38 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5117 Z= 0.113 Angle : 0.626 9.144 6969 Z= 0.301 Chirality : 0.041 0.171 790 Planarity : 0.005 0.058 897 Dihedral : 4.747 29.607 712 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 4.33 % Allowed : 26.18 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.35), residues: 634 helix: 1.26 (0.30), residues: 339 sheet: 0.77 (0.64), residues: 52 loop : -1.28 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.007 0.001 TYR B 77 PHE 0.009 0.001 PHE A 117 TRP 0.007 0.001 TRP B 119 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 5117) covalent geometry : angle 0.62559 / 0.30 ( 6969) hydrogen bonds : bond 0.03188 / 2.23 ( 246) hydrogen bonds : angle 3.74609 / 2.69 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8900 (mm-40) REVERT: A 120 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8359 (ptp) REVERT: A 155 VAL cc_start: 0.9133 (t) cc_final: 0.8885 (m) REVERT: A 184 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9120 (mm110) REVERT: A 188 ASN cc_start: 0.9504 (m110) cc_final: 0.9065 (p0) REVERT: A 248 LEU cc_start: 0.8942 (tp) cc_final: 0.8724 (tp) REVERT: A 282 GLU cc_start: 0.8751 (mp0) cc_final: 0.8473 (tp30) REVERT: B 89 LEU cc_start: 0.8590 (tp) cc_final: 0.8330 (tt) REVERT: B 120 MET cc_start: 0.8154 (ptm) cc_final: 0.7742 (ptm) REVERT: B 206 CYS cc_start: 0.9436 (m) cc_final: 0.9215 (m) REVERT: B 216 ASP cc_start: 0.8945 (t0) cc_final: 0.8397 (t0) REVERT: B 271 MET cc_start: 0.8859 (mmm) cc_final: 0.8606 (mmm) REVERT: B 283 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8380 (p0) REVERT: B 325 LEU cc_start: 0.9438 (tt) cc_final: 0.9222 (mt) outliers start: 23 outliers final: 14 residues processed: 112 average time/residue: 0.0514 time to fit residues: 8.2385 Evaluate side-chains 109 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 0.1980 chunk 52 optimal weight: 0.0570 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069240 restraints weight = 13754.742| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 5.38 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5117 Z= 0.103 Angle : 0.624 9.803 6969 Z= 0.291 Chirality : 0.040 0.158 790 Planarity : 0.004 0.056 897 Dihedral : 4.545 28.743 712 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.79 % Rotamer: Outliers : 4.14 % Allowed : 25.61 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.35), residues: 634 helix: 1.44 (0.30), residues: 340 sheet: 0.75 (0.64), residues: 52 loop : -1.18 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.006 0.001 TYR B 77 PHE 0.008 0.000 PHE A 117 TRP 0.006 0.001 TRP A 119 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 5117) covalent geometry : angle 0.62379 / 0.29 ( 6969) hydrogen bonds : bond 0.02880 / 2.02 ( 246) hydrogen bonds : angle 3.61270 / 2.59 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9273 (mm-40) cc_final: 0.9067 (mm-40) REVERT: A 120 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8293 (ptp) REVERT: A 155 VAL cc_start: 0.9030 (t) cc_final: 0.8792 (m) REVERT: A 184 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.9145 (mm110) REVERT: A 188 ASN cc_start: 0.9511 (m110) cc_final: 0.9075 (p0) REVERT: A 202 LEU cc_start: 0.9375 (mm) cc_final: 0.9150 (mt) REVERT: B 89 LEU cc_start: 0.8292 (tp) cc_final: 0.8010 (tt) REVERT: B 120 MET cc_start: 0.8260 (ptm) cc_final: 0.7626 (ptm) REVERT: B 143 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8787 (pt0) REVERT: B 206 CYS cc_start: 0.9388 (m) cc_final: 0.9154 (m) REVERT: B 216 ASP cc_start: 0.8955 (t0) cc_final: 0.8410 (t0) REVERT: B 286 GLU cc_start: 0.8929 (mp0) cc_final: 0.8618 (mp0) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.0560 time to fit residues: 8.5953 Evaluate side-chains 108 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067900 restraints weight = 14073.755| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 5.27 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5117 Z= 0.146 Angle : 0.629 7.116 6969 Z= 0.305 Chirality : 0.042 0.167 790 Planarity : 0.005 0.056 897 Dihedral : 4.542 29.204 712 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 5.65 % Allowed : 24.67 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.35), residues: 634 helix: 1.41 (0.30), residues: 346 sheet: 1.11 (0.73), residues: 40 loop : -1.02 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.007 0.001 TYR B 77 PHE 0.018 0.001 PHE A 117 TRP 0.007 0.001 TRP A 119 HIS 0.002 0.001 HIS B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 5117) covalent geometry : angle 0.62863 / 0.30 ( 6969) hydrogen bonds : bond 0.03455 / 2.42 ( 246) hydrogen bonds : angle 3.67123 / 2.63 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.233 Fit side-chains REVERT: A 55 GLN cc_start: 0.9322 (mm-40) cc_final: 0.9069 (mm-40) REVERT: A 120 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8405 (ptp) REVERT: A 184 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.9201 (mm110) REVERT: A 188 ASN cc_start: 0.9528 (m110) cc_final: 0.9101 (p0) REVERT: B 89 LEU cc_start: 0.8704 (tp) cc_final: 0.8417 (tt) REVERT: B 120 MET cc_start: 0.8321 (ptm) cc_final: 0.7833 (ptm) REVERT: B 206 CYS cc_start: 0.9392 (m) cc_final: 0.9069 (m) REVERT: B 216 ASP cc_start: 0.8980 (t0) cc_final: 0.8436 (t0) REVERT: B 283 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.8469 (p0) outliers start: 30 outliers final: 21 residues processed: 109 average time/residue: 0.0505 time to fit residues: 7.8634 Evaluate side-chains 109 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 0.1980 chunk 40 optimal weight: 0.0020 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068640 restraints weight = 14101.841| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 5.50 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5117 Z= 0.106 Angle : 0.643 10.595 6969 Z= 0.297 Chirality : 0.041 0.244 790 Planarity : 0.004 0.055 897 Dihedral : 4.403 28.639 712 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 4.14 % Allowed : 27.12 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.35), residues: 634 helix: 1.42 (0.30), residues: 346 sheet: 1.05 (0.71), residues: 40 loop : -0.96 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.006 0.001 TYR B 77 PHE 0.016 0.001 PHE A 117 TRP 0.007 0.001 TRP A 119 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 5117) covalent geometry : angle 0.64304 / 0.30 ( 6969) hydrogen bonds : bond 0.02986 / 2.09 ( 246) hydrogen bonds : angle 3.54472 / 2.54 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.173 Fit side-chains REVERT: A 120 MET cc_start: 0.8815 (ptt) cc_final: 0.8314 (ptp) REVERT: A 184 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.9189 (mm110) REVERT: A 188 ASN cc_start: 0.9540 (m110) cc_final: 0.9110 (p0) REVERT: B 89 LEU cc_start: 0.8213 (tp) cc_final: 0.7897 (tt) REVERT: B 120 MET cc_start: 0.8265 (ptm) cc_final: 0.7883 (ptm) REVERT: B 143 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8768 (pt0) REVERT: B 206 CYS cc_start: 0.9359 (m) cc_final: 0.9063 (m) REVERT: B 216 ASP cc_start: 0.8916 (t0) cc_final: 0.8363 (t0) REVERT: B 271 MET cc_start: 0.8884 (mmm) cc_final: 0.8571 (mmm) REVERT: B 283 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8437 (p0) REVERT: B 286 GLU cc_start: 0.8976 (mp0) cc_final: 0.8698 (mp0) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.0468 time to fit residues: 7.0499 Evaluate side-chains 105 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 16 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.064092 restraints weight = 14123.868| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 5.28 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5117 Z= 0.180 Angle : 0.664 7.197 6969 Z= 0.321 Chirality : 0.043 0.264 790 Planarity : 0.005 0.056 897 Dihedral : 4.498 29.413 712 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 5.27 % Allowed : 26.18 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.35), residues: 634 helix: 1.46 (0.30), residues: 345 sheet: 1.99 (0.78), residues: 28 loop : -0.91 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.009 0.001 TYR B 46 PHE 0.016 0.001 PHE A 117 TRP 0.009 0.002 TRP B 119 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 5117) covalent geometry : angle 0.66449 / 0.32 ( 6969) hydrogen bonds : bond 0.03790 / 2.64 ( 246) hydrogen bonds : angle 3.76496 / 2.70 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.185 Fit side-chains REVERT: A 20 LYS cc_start: 0.8815 (mttt) cc_final: 0.8265 (mmtt) REVERT: A 120 MET cc_start: 0.8911 (ptt) cc_final: 0.8361 (ptp) REVERT: A 184 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.9231 (mm110) REVERT: A 188 ASN cc_start: 0.9564 (m110) cc_final: 0.9133 (p0) REVERT: B 20 LYS cc_start: 0.8124 (mttt) cc_final: 0.7796 (tttm) REVERT: B 89 LEU cc_start: 0.8824 (tp) cc_final: 0.8616 (tt) REVERT: B 120 MET cc_start: 0.8356 (ptm) cc_final: 0.7991 (ptm) REVERT: B 143 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8660 (pt0) REVERT: B 206 CYS cc_start: 0.9362 (m) cc_final: 0.9079 (m) REVERT: B 216 ASP cc_start: 0.9023 (t0) cc_final: 0.8379 (t0) outliers start: 28 outliers final: 22 residues processed: 104 average time/residue: 0.0553 time to fit residues: 8.0068 Evaluate side-chains 102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.0670 chunk 63 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068304 restraints weight = 14054.117| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 5.27 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5117 Z= 0.113 Angle : 0.668 10.227 6969 Z= 0.306 Chirality : 0.042 0.283 790 Planarity : 0.004 0.055 897 Dihedral : 4.402 28.930 712 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 4.14 % Allowed : 27.50 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.35), residues: 634 helix: 1.57 (0.30), residues: 339 sheet: 2.07 (0.76), residues: 28 loop : -0.88 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.008 0.001 TYR B 77 PHE 0.015 0.001 PHE A 117 TRP 0.010 0.002 TRP B 161 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 5117) covalent geometry : angle 0.66822 / 0.31 ( 6969) hydrogen bonds : bond 0.03165 / 2.20 ( 246) hydrogen bonds : angle 3.57099 / 2.55 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.203 Fit side-chains REVERT: A 120 MET cc_start: 0.8841 (ptt) cc_final: 0.8335 (ptp) REVERT: A 143 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: A 184 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.9153 (mm110) REVERT: A 188 ASN cc_start: 0.9560 (m110) cc_final: 0.9223 (p0) REVERT: A 272 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8873 (p) REVERT: B 20 LYS cc_start: 0.8115 (mttt) cc_final: 0.7667 (tttm) REVERT: B 89 LEU cc_start: 0.8340 (tp) cc_final: 0.8008 (tt) REVERT: B 120 MET cc_start: 0.8293 (ptm) cc_final: 0.7969 (ptm) REVERT: B 143 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8775 (pt0) REVERT: B 206 CYS cc_start: 0.9269 (m) cc_final: 0.8950 (m) REVERT: B 216 ASP cc_start: 0.9010 (t0) cc_final: 0.8377 (t0) REVERT: B 271 MET cc_start: 0.8831 (mmm) cc_final: 0.8556 (mmm) REVERT: B 283 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8589 (p0) REVERT: B 286 GLU cc_start: 0.8940 (mp0) cc_final: 0.8718 (mp0) outliers start: 22 outliers final: 17 residues processed: 96 average time/residue: 0.0520 time to fit residues: 7.1597 Evaluate side-chains 103 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 35 optimal weight: 0.0000 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067169 restraints weight = 14050.150| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 5.29 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5117 Z= 0.125 Angle : 0.662 10.091 6969 Z= 0.306 Chirality : 0.042 0.279 790 Planarity : 0.005 0.055 897 Dihedral : 4.357 28.991 712 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 4.14 % Allowed : 27.87 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.35), residues: 634 helix: 1.56 (0.30), residues: 339 sheet: 1.45 (0.65), residues: 40 loop : -0.86 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.008 0.001 TYR B 77 PHE 0.014 0.001 PHE A 117 TRP 0.010 0.002 TRP B 161 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 5117) covalent geometry : angle 0.66238 / 0.31 ( 6969) hydrogen bonds : bond 0.03264 / 2.29 ( 246) hydrogen bonds : angle 3.60206 / 2.57 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.200 Fit side-chains REVERT: A 120 MET cc_start: 0.8858 (ptt) cc_final: 0.8294 (ptp) REVERT: A 143 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8629 (mt-10) REVERT: A 184 GLN cc_start: 0.9526 (OUTLIER) cc_final: 0.9164 (mm110) REVERT: A 188 ASN cc_start: 0.9579 (m110) cc_final: 0.9238 (p0) REVERT: B 20 LYS cc_start: 0.8135 (mttt) cc_final: 0.7804 (tttm) REVERT: B 89 LEU cc_start: 0.8420 (tp) cc_final: 0.8095 (tt) REVERT: B 120 MET cc_start: 0.8309 (ptm) cc_final: 0.7992 (ptm) REVERT: B 143 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8778 (pt0) REVERT: B 206 CYS cc_start: 0.9245 (m) cc_final: 0.8925 (m) REVERT: B 216 ASP cc_start: 0.8991 (t0) cc_final: 0.8347 (t0) REVERT: B 271 MET cc_start: 0.8896 (mmm) cc_final: 0.8595 (mmm) REVERT: B 283 ASP cc_start: 0.9284 (OUTLIER) cc_final: 0.8576 (p0) REVERT: B 286 GLU cc_start: 0.8960 (mp0) cc_final: 0.8711 (mp0) outliers start: 22 outliers final: 17 residues processed: 96 average time/residue: 0.0472 time to fit residues: 6.5139 Evaluate side-chains 98 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067334 restraints weight = 13946.758| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 5.24 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5117 Z= 0.111 Angle : 0.674 10.211 6969 Z= 0.307 Chirality : 0.041 0.272 790 Planarity : 0.004 0.055 897 Dihedral : 4.280 28.599 712 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 3.77 % Allowed : 28.25 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.35), residues: 634 helix: 1.55 (0.30), residues: 339 sheet: 1.44 (0.67), residues: 40 loop : -0.87 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.007 0.001 TYR B 77 PHE 0.014 0.001 PHE A 117 TRP 0.009 0.001 TRP B 161 HIS 0.001 0.000 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5117) covalent geometry : angle 0.67368 / 0.31 ( 6969) hydrogen bonds : bond 0.02990 / 2.09 ( 246) hydrogen bonds : angle 3.56062 / 2.54 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.188 Fit side-chains REVERT: A 120 MET cc_start: 0.8838 (ptt) cc_final: 0.8354 (ptp) REVERT: A 184 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.9173 (mm110) REVERT: A 188 ASN cc_start: 0.9593 (m110) cc_final: 0.9264 (p0) REVERT: B 20 LYS cc_start: 0.8129 (mttt) cc_final: 0.7704 (tttm) REVERT: B 89 LEU cc_start: 0.8273 (tp) cc_final: 0.7935 (tt) REVERT: B 120 MET cc_start: 0.8338 (ptm) cc_final: 0.7972 (ptm) REVERT: B 143 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8743 (pt0) REVERT: B 206 CYS cc_start: 0.9211 (m) cc_final: 0.8895 (m) REVERT: B 216 ASP cc_start: 0.8997 (t0) cc_final: 0.8493 (t0) REVERT: B 271 MET cc_start: 0.8876 (mmm) cc_final: 0.8591 (mmm) REVERT: B 283 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.8555 (p0) REVERT: B 286 GLU cc_start: 0.8932 (mp0) cc_final: 0.8676 (mp0) outliers start: 20 outliers final: 18 residues processed: 93 average time/residue: 0.0514 time to fit residues: 6.7637 Evaluate side-chains 100 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.084922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.063374 restraints weight = 14299.455| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 5.06 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5117 Z= 0.204 Angle : 0.724 9.506 6969 Z= 0.342 Chirality : 0.043 0.156 790 Planarity : 0.005 0.056 897 Dihedral : 4.506 29.756 712 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 4.33 % Allowed : 27.31 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.35), residues: 634 helix: 1.51 (0.30), residues: 339 sheet: 2.24 (0.76), residues: 28 loop : -0.79 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 78 TYR 0.011 0.001 TYR B 46 PHE 0.013 0.001 PHE A 117 TRP 0.015 0.002 TRP A 34 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 ( 5117) covalent geometry : angle 0.72449 / 0.34 ( 6969) hydrogen bonds : bond 0.04073 / 2.84 ( 246) hydrogen bonds : angle 3.87210 / 2.76 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 973.81 seconds wall clock time: 17 minutes 29.37 seconds (1049.37 seconds total)