Starting phenix.real_space_refine on Fri Aug 22 17:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7r_36939/08_2025/8k7r_36939.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7r_36939/08_2025/8k7r_36939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k7r_36939/08_2025/8k7r_36939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7r_36939/08_2025/8k7r_36939.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7r_36939/08_2025/8k7r_36939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7r_36939/08_2025/8k7r_36939.cif" } resolution = 3.56 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 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= 0.002 sd= 0.056 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 27 5.16 5 C 4051 2.51 5 N 1100 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6472 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1448 Classifications: {'peptide': 175} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 167} Chain: "E" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2382 Classifications: {'peptide': 304} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2376 Classifications: {'peptide': 303} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.53, per 1000 atoms: 0.24 Number of scatterers: 6472 At special positions: 0 Unit cell: (102.367, 99.6, 124.5, 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 27 16.00 O 1294 8.00 N 1100 7.00 C 4051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS F 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 209 " - pdb=" SG CYS F 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 405 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 239 " - pdb=" SG CYS F 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 345 " - pdb=" SG CYS F 405 " distance=2.03 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 301 " - " ASN A 191 " " NAG A 302 " - " ASN A 165 " " NAG B 1 " - " ASN A 46 " " NAG C 1 " - " ASN A 160 " " NAG D 1 " - " ASN A 67 " " NAG G 1 " - " ASN E 275 " " NAG H 1 " - " ASN F 275 " Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 332.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 19 sheets defined 8.1% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.763A pdb=" N SER A 88 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.563A pdb=" N GLY E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 393 through 399 removed outlier: 3.646A pdb=" N GLN E 399 " --> pdb=" O ALA E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 187 Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'F' and resid 287 through 294 Processing helix chain 'F' and resid 394 through 399 removed outlier: 3.577A pdb=" N GLN F 399 " --> pdb=" O ALA F 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.405A pdb=" N ILE A 41 " --> pdb=" O PHE A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 155 removed outlier: 3.917A pdb=" N GLU A 150 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 145 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 154 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 143 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYS A 142 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS A 179 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA7, first strand: chain 'E' and resid 178 through 179 removed outlier: 6.448A pdb=" N GLN E 132 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 157 through 161 removed outlier: 4.964A pdb=" N GLN E 146 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 218 through 221 removed outlier: 3.731A pdb=" N ASP E 243 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU E 278 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR E 279 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR E 283 " --> pdb=" O THR E 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 253 through 257 Processing sheet with id=AB2, first strand: chain 'E' and resid 325 through 330 Processing sheet with id=AB3, first strand: chain 'E' and resid 325 through 330 Processing sheet with id=AB4, first strand: chain 'E' and resid 364 through 365 Processing sheet with id=AB5, first strand: chain 'F' and resid 146 through 151 removed outlier: 3.996A pdb=" N GLN F 146 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 218 through 222 removed outlier: 3.863A pdb=" N THR F 238 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 252 through 257 Processing sheet with id=AB8, first strand: chain 'F' and resid 325 through 330 removed outlier: 6.039A pdb=" N PHE F 384 " --> pdb=" O ASN F 349 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 325 through 330 removed outlier: 6.039A pdb=" N PHE F 384 " --> pdb=" O ASN F 349 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 364 through 365 250 hydrogen bonds defined for protein. 633 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: 0.95 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2063 1.35 - 1.47: 1655 1.47 - 1.58: 2878 1.58 - 1.70: 2 1.70 - 1.82: 34 Bond restraints: 6632 Sorted by residual: bond pdb=" CG PRO F 332 " pdb=" CD PRO F 332 " ideal model delta sigma weight residual 1.503 1.329 0.174 3.40e-02 8.65e+02 2.62e+01 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CB PRO F 332 " pdb=" CG PRO F 332 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.22e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.582 -0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" CB PRO E 332 " pdb=" CG PRO E 332 " ideal model delta sigma weight residual 1.492 1.649 -0.157 5.00e-02 4.00e+02 9.90e+00 ... (remaining 6627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 8958 3.45 - 6.90: 62 6.90 - 10.35: 6 10.35 - 13.80: 1 13.80 - 17.25: 2 Bond angle restraints: 9029 Sorted by residual: angle pdb=" CA PRO F 332 " pdb=" N PRO F 332 " pdb=" CD PRO F 332 " ideal model delta sigma weight residual 112.00 94.75 17.25 1.40e+00 5.10e-01 1.52e+02 angle pdb=" CA PRO E 332 " pdb=" N PRO E 332 " pdb=" CD PRO E 332 " ideal model delta sigma weight residual 112.00 97.91 14.09 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N PRO F 332 " pdb=" CD PRO F 332 " pdb=" CG PRO F 332 " ideal model delta sigma weight residual 103.20 92.52 10.68 1.50e+00 4.44e-01 5.07e+01 angle pdb=" N PRO E 332 " pdb=" CD PRO E 332 " pdb=" CG PRO E 332 " ideal model delta sigma weight residual 103.20 95.98 7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" CA PRO F 332 " pdb=" CB PRO F 332 " pdb=" CG PRO F 332 " ideal model delta sigma weight residual 104.50 95.72 8.78 1.90e+00 2.77e-01 2.13e+01 ... (remaining 9024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 3853 24.62 - 49.24: 306 49.24 - 73.86: 44 73.86 - 98.48: 32 98.48 - 123.10: 21 Dihedral angle restraints: 4256 sinusoidal: 1980 harmonic: 2276 Sorted by residual: dihedral pdb=" CB CYS E 121 " pdb=" SG CYS E 121 " pdb=" SG CYS F 209 " pdb=" CB CYS F 209 " ideal model delta sinusoidal sigma weight residual -86.00 -0.49 -85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CA PRO E 332 " pdb=" C PRO E 332 " pdb=" N GLU E 333 " pdb=" CA GLU E 333 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual -86.00 -122.08 36.08 1 1.00e+01 1.00e-02 1.84e+01 ... (remaining 4253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 883 0.055 - 0.109: 143 0.109 - 0.164: 31 0.164 - 0.219: 3 0.219 - 0.273: 4 Chirality restraints: 1064 Sorted by residual: chirality pdb=" C2 BMA D 3 " pdb=" C1 BMA D 3 " pdb=" C3 BMA D 3 " pdb=" O2 BMA D 3 " both_signs ideal model delta sigma weight residual False 2.47 2.75 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1061 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 331 " 0.088 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO F 332 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO F 332 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 332 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 331 " 0.074 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO E 332 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 306 " 0.060 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO E 307 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 307 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 307 " 0.048 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 259 2.72 - 3.26: 5807 3.26 - 3.81: 9886 3.81 - 4.35: 11995 4.35 - 4.90: 20782 Nonbonded interactions: 48729 Sorted by model distance: nonbonded pdb=" OH TYR F 140 " pdb=" OG1 THR F 174 " model vdw 2.173 3.040 nonbonded pdb=" O PHE A 57 " pdb=" OG SER A 61 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR F 148 " pdb=" OE1 GLN F 194 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR E 140 " pdb=" O ALA E 172 " model vdw 2.299 3.040 nonbonded pdb=" O SER F 234 " pdb=" OG SER F 234 " model vdw 2.326 3.040 ... (remaining 48724 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 'E' and (resid 113 through 159 or resid 172 through 257 or (resid 258 and \ (name N or name CA or name C or name O )) or resid 259 through 425)) selection = (chain 'F' and (resid 113 through 231 or (resid 232 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ )) or resi \ d 233 through 425)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.030 Process input model: 7.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.006 0.174 6663 Z= 0.222 Angle : 0.792 17.253 9112 Z= 0.395 Chirality : 0.048 0.273 1064 Planarity : 0.006 0.119 1127 Dihedral : 20.110 123.105 2750 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.90 % Favored : 91.84 % Rotamer: Outliers : 0.43 % Allowed : 20.31 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.22 (0.31), residues: 772 helix: -1.05 (0.90), residues: 35 sheet: 1.15 (0.28), residues: 353 loop : -0.71 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 341 TYR 0.006 0.001 TYR A 175 PHE 0.016 0.001 PHE E 329 TRP 0.008 0.001 TRP A 181 HIS 0.008 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 6632) covalent geometry : angle 0.77454 ( 9029) SS BOND : bond 0.00246 ( 10) SS BOND : angle 0.68021 ( 20) hydrogen bonds : bond 0.10931 ( 221) hydrogen bonds : angle 5.43966 ( 633) link_ALPHA1-3 : bond 0.00907 ( 3) link_ALPHA1-3 : angle 2.65000 ( 9) link_ALPHA1-6 : bond 0.00665 ( 2) link_ALPHA1-6 : angle 1.36746 ( 6) link_BETA1-4 : bond 0.01113 ( 8) link_BETA1-4 : angle 2.41432 ( 24) link_BETA1-6 : bond 0.00362 ( 1) link_BETA1-6 : angle 1.30001 ( 3) link_NAG-ASN : bond 0.00212 ( 7) link_NAG-ASN : angle 1.81628 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 191 TYR cc_start: 0.8290 (m-80) cc_final: 0.7834 (m-80) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.0678 time to fit residues: 7.1637 Evaluate side-chains 76 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain F residue 146 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN F 182 GLN F 194 GLN F 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.110526 restraints weight = 8302.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112745 restraints weight = 6264.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114113 restraints weight = 5280.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114760 restraints weight = 4738.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114760 restraints weight = 4457.458| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6663 Z= 0.260 Angle : 0.747 10.216 9112 Z= 0.356 Chirality : 0.049 0.254 1064 Planarity : 0.005 0.050 1127 Dihedral : 16.359 106.978 1269 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.07 % Favored : 90.67 % Rotamer: Outliers : 4.15 % Allowed : 18.31 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.01 (0.30), residues: 772 helix: -1.13 (0.75), residues: 43 sheet: 1.08 (0.27), residues: 359 loop : -0.95 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 131 TYR 0.019 0.002 TYR E 327 PHE 0.011 0.002 PHE E 329 TRP 0.011 0.002 TRP A 38 HIS 0.008 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 6632) covalent geometry : angle 0.70966 ( 9029) SS BOND : bond 0.00218 ( 10) SS BOND : angle 1.13453 ( 20) hydrogen bonds : bond 0.03577 ( 221) hydrogen bonds : angle 4.79894 ( 633) link_ALPHA1-3 : bond 0.01260 ( 3) link_ALPHA1-3 : angle 3.42190 ( 9) link_ALPHA1-6 : bond 0.00680 ( 2) link_ALPHA1-6 : angle 1.75176 ( 6) link_BETA1-4 : bond 0.01165 ( 8) link_BETA1-4 : angle 3.06565 ( 24) link_BETA1-6 : bond 0.00185 ( 1) link_BETA1-6 : angle 1.08461 ( 3) link_NAG-ASN : bond 0.00289 ( 7) link_NAG-ASN : angle 2.78116 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8059 (ttt180) REVERT: A 169 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: E 256 SER cc_start: 0.9081 (p) cc_final: 0.8724 (t) REVERT: E 311 MET cc_start: 0.7058 (tpp) cc_final: 0.6580 (tpt) REVERT: F 306 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8633 (mp) outliers start: 29 outliers final: 8 residues processed: 100 average time/residue: 0.0837 time to fit residues: 11.1880 Evaluate side-chains 81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 202 PHE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.160104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114866 restraints weight = 8155.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117476 restraints weight = 5804.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118821 restraints weight = 4708.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119992 restraints weight = 4177.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120510 restraints weight = 3876.144| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6663 Z= 0.133 Angle : 0.655 9.822 9112 Z= 0.309 Chirality : 0.046 0.250 1064 Planarity : 0.004 0.038 1127 Dihedral : 15.159 105.495 1264 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.81 % Favored : 90.80 % Rotamer: Outliers : 1.57 % Allowed : 19.03 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.02 (0.30), residues: 772 helix: -1.18 (0.77), residues: 42 sheet: 1.09 (0.27), residues: 349 loop : -0.89 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 289 TYR 0.015 0.001 TYR F 197 PHE 0.009 0.001 PHE F 350 TRP 0.008 0.001 TRP F 291 HIS 0.006 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6632) covalent geometry : angle 0.62199 ( 9029) SS BOND : bond 0.00139 ( 10) SS BOND : angle 0.67452 ( 20) hydrogen bonds : bond 0.02943 ( 221) hydrogen bonds : angle 4.59088 ( 633) link_ALPHA1-3 : bond 0.01386 ( 3) link_ALPHA1-3 : angle 3.13486 ( 9) link_ALPHA1-6 : bond 0.01037 ( 2) link_ALPHA1-6 : angle 1.53227 ( 6) link_BETA1-4 : bond 0.01208 ( 8) link_BETA1-4 : angle 2.76080 ( 24) link_BETA1-6 : bond 0.00195 ( 1) link_BETA1-6 : angle 1.23318 ( 3) link_NAG-ASN : bond 0.00150 ( 7) link_NAG-ASN : angle 2.33641 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 256 SER cc_start: 0.9136 (p) cc_final: 0.8727 (t) REVERT: E 311 MET cc_start: 0.7167 (tpp) cc_final: 0.6737 (tpt) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 0.0680 time to fit residues: 7.7872 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 317 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 0.0170 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.159154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114084 restraints weight = 8263.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.116729 restraints weight = 6180.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116885 restraints weight = 4939.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117978 restraints weight = 4633.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117957 restraints weight = 4522.799| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6663 Z= 0.160 Angle : 0.677 10.193 9112 Z= 0.319 Chirality : 0.046 0.260 1064 Planarity : 0.004 0.035 1127 Dihedral : 14.427 102.820 1264 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.68 % Favored : 91.06 % Rotamer: Outliers : 2.29 % Allowed : 18.31 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.00 (0.31), residues: 772 helix: -1.23 (0.76), residues: 42 sheet: 1.06 (0.27), residues: 355 loop : -0.92 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 289 TYR 0.008 0.001 TYR A 174 PHE 0.014 0.001 PHE E 329 TRP 0.008 0.001 TRP A 38 HIS 0.005 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6632) covalent geometry : angle 0.64333 ( 9029) SS BOND : bond 0.00195 ( 10) SS BOND : angle 0.75573 ( 20) hydrogen bonds : bond 0.02877 ( 221) hydrogen bonds : angle 4.55700 ( 633) link_ALPHA1-3 : bond 0.01366 ( 3) link_ALPHA1-3 : angle 3.11519 ( 9) link_ALPHA1-6 : bond 0.01007 ( 2) link_ALPHA1-6 : angle 1.51032 ( 6) link_BETA1-4 : bond 0.01210 ( 8) link_BETA1-4 : angle 2.87330 ( 24) link_BETA1-6 : bond 0.00227 ( 1) link_BETA1-6 : angle 1.29914 ( 3) link_NAG-ASN : bond 0.00146 ( 7) link_NAG-ASN : angle 2.37895 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 183 LYS cc_start: 0.7372 (mttt) cc_final: 0.6937 (tttt) REVERT: E 256 SER cc_start: 0.9073 (p) cc_final: 0.8679 (t) REVERT: E 311 MET cc_start: 0.7073 (tpp) cc_final: 0.6686 (tpt) outliers start: 16 outliers final: 8 residues processed: 83 average time/residue: 0.0734 time to fit residues: 8.4532 Evaluate side-chains 73 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.161286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115859 restraints weight = 8272.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.117877 restraints weight = 6169.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118320 restraints weight = 5200.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118845 restraints weight = 4656.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119123 restraints weight = 4706.979| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6663 Z= 0.122 Angle : 0.658 9.784 9112 Z= 0.308 Chirality : 0.046 0.273 1064 Planarity : 0.003 0.030 1127 Dihedral : 13.440 99.704 1264 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.68 % Favored : 91.06 % Rotamer: Outliers : 2.43 % Allowed : 19.03 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.01 (0.31), residues: 772 helix: -1.26 (0.76), residues: 42 sheet: 1.06 (0.27), residues: 347 loop : -0.85 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 289 TYR 0.008 0.001 TYR A 174 PHE 0.008 0.001 PHE F 350 TRP 0.008 0.001 TRP F 291 HIS 0.002 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6632) covalent geometry : angle 0.62465 ( 9029) SS BOND : bond 0.00343 ( 10) SS BOND : angle 0.72746 ( 20) hydrogen bonds : bond 0.02716 ( 221) hydrogen bonds : angle 4.47293 ( 633) link_ALPHA1-3 : bond 0.01514 ( 3) link_ALPHA1-3 : angle 3.18852 ( 9) link_ALPHA1-6 : bond 0.01083 ( 2) link_ALPHA1-6 : angle 1.84182 ( 6) link_BETA1-4 : bond 0.01216 ( 8) link_BETA1-4 : angle 2.77349 ( 24) link_BETA1-6 : bond 0.00196 ( 1) link_BETA1-6 : angle 1.28947 ( 3) link_NAG-ASN : bond 0.00168 ( 7) link_NAG-ASN : angle 2.26597 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 183 LYS cc_start: 0.7458 (mttt) cc_final: 0.6944 (tttt) REVERT: E 256 SER cc_start: 0.9098 (p) cc_final: 0.8668 (t) REVERT: E 264 ASN cc_start: 0.8157 (m-40) cc_final: 0.7882 (m110) REVERT: E 311 MET cc_start: 0.7032 (tpp) cc_final: 0.6666 (tpt) REVERT: F 149 TRP cc_start: 0.8528 (m100) cc_final: 0.8275 (m100) outliers start: 17 outliers final: 10 residues processed: 88 average time/residue: 0.0629 time to fit residues: 7.5680 Evaluate side-chains 77 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 95 HIS ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116779 restraints weight = 8227.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118929 restraints weight = 6282.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.119541 restraints weight = 4964.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120004 restraints weight = 4649.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120205 restraints weight = 4606.236| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6663 Z= 0.117 Angle : 0.655 9.811 9112 Z= 0.308 Chirality : 0.045 0.284 1064 Planarity : 0.003 0.029 1127 Dihedral : 12.377 95.340 1264 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.42 % Favored : 91.19 % Rotamer: Outliers : 1.57 % Allowed : 20.31 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.04 (0.31), residues: 772 helix: -1.48 (0.75), residues: 43 sheet: 1.03 (0.27), residues: 350 loop : -0.76 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 289 TYR 0.006 0.001 TYR A 174 PHE 0.008 0.001 PHE E 385 TRP 0.008 0.001 TRP A 181 HIS 0.003 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6632) covalent geometry : angle 0.62044 ( 9029) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.71851 ( 20) hydrogen bonds : bond 0.02602 ( 221) hydrogen bonds : angle 4.32075 ( 633) link_ALPHA1-3 : bond 0.01577 ( 3) link_ALPHA1-3 : angle 3.35412 ( 9) link_ALPHA1-6 : bond 0.00832 ( 2) link_ALPHA1-6 : angle 1.67054 ( 6) link_BETA1-4 : bond 0.01224 ( 8) link_BETA1-4 : angle 2.85027 ( 24) link_BETA1-6 : bond 0.00238 ( 1) link_BETA1-6 : angle 1.26012 ( 3) link_NAG-ASN : bond 0.00153 ( 7) link_NAG-ASN : angle 2.20277 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6760 (ttpt) REVERT: E 183 LYS cc_start: 0.7474 (mttt) cc_final: 0.7115 (tttt) REVERT: E 189 ARG cc_start: 0.5954 (mmm-85) cc_final: 0.5568 (mmm-85) REVERT: E 264 ASN cc_start: 0.8154 (m-40) cc_final: 0.7879 (m110) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 0.0704 time to fit residues: 7.9864 Evaluate side-chains 71 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS E 252 GLN ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.160220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115091 restraints weight = 8098.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117567 restraints weight = 5794.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119132 restraints weight = 4715.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119916 restraints weight = 4188.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120477 restraints weight = 3908.039| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6663 Z= 0.137 Angle : 0.661 10.008 9112 Z= 0.311 Chirality : 0.046 0.291 1064 Planarity : 0.003 0.027 1127 Dihedral : 12.059 92.993 1264 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.68 % Favored : 90.93 % Rotamer: Outliers : 2.29 % Allowed : 19.89 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: -0.01 (0.30), residues: 772 helix: -1.49 (0.74), residues: 43 sheet: 1.00 (0.27), residues: 346 loop : -0.78 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 289 TYR 0.017 0.001 TYR E 327 PHE 0.008 0.001 PHE E 385 TRP 0.007 0.001 TRP A 181 HIS 0.003 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6632) covalent geometry : angle 0.62573 ( 9029) SS BOND : bond 0.00193 ( 10) SS BOND : angle 0.59643 ( 20) hydrogen bonds : bond 0.02736 ( 221) hydrogen bonds : angle 4.30699 ( 633) link_ALPHA1-3 : bond 0.01499 ( 3) link_ALPHA1-3 : angle 3.34258 ( 9) link_ALPHA1-6 : bond 0.00710 ( 2) link_ALPHA1-6 : angle 1.88831 ( 6) link_BETA1-4 : bond 0.01195 ( 8) link_BETA1-4 : angle 2.90022 ( 24) link_BETA1-6 : bond 0.00215 ( 1) link_BETA1-6 : angle 1.27377 ( 3) link_NAG-ASN : bond 0.00105 ( 7) link_NAG-ASN : angle 2.35152 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7072 (ttpt) cc_final: 0.6868 (ttpt) REVERT: A 131 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8023 (ttt180) REVERT: E 183 LYS cc_start: 0.7551 (mttt) cc_final: 0.7180 (tttt) REVERT: E 256 SER cc_start: 0.9092 (p) cc_final: 0.8722 (t) REVERT: F 311 MET cc_start: 0.7543 (tpt) cc_final: 0.7092 (tpp) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 0.0788 time to fit residues: 8.8836 Evaluate side-chains 77 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.161235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.115050 restraints weight = 8195.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.117470 restraints weight = 6156.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118946 restraints weight = 5086.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119664 restraints weight = 4530.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.119803 restraints weight = 4268.470| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6663 Z= 0.126 Angle : 0.661 9.963 9112 Z= 0.310 Chirality : 0.045 0.292 1064 Planarity : 0.003 0.027 1127 Dihedral : 11.547 89.246 1264 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.16 % Favored : 91.45 % Rotamer: Outliers : 2.43 % Allowed : 20.03 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.00 (0.30), residues: 772 helix: -1.48 (0.75), residues: 43 sheet: 0.99 (0.27), residues: 346 loop : -0.75 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 289 TYR 0.011 0.001 TYR E 327 PHE 0.010 0.001 PHE F 329 TRP 0.007 0.001 TRP A 181 HIS 0.003 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6632) covalent geometry : angle 0.62604 ( 9029) SS BOND : bond 0.00195 ( 10) SS BOND : angle 0.57860 ( 20) hydrogen bonds : bond 0.02626 ( 221) hydrogen bonds : angle 4.26262 ( 633) link_ALPHA1-3 : bond 0.01514 ( 3) link_ALPHA1-3 : angle 3.34008 ( 9) link_ALPHA1-6 : bond 0.00723 ( 2) link_ALPHA1-6 : angle 1.67481 ( 6) link_BETA1-4 : bond 0.01193 ( 8) link_BETA1-4 : angle 2.90077 ( 24) link_BETA1-6 : bond 0.00184 ( 1) link_BETA1-6 : angle 1.28692 ( 3) link_NAG-ASN : bond 0.00116 ( 7) link_NAG-ASN : angle 2.32889 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.7824 (m-10) cc_final: 0.7577 (m-10) REVERT: E 183 LYS cc_start: 0.7615 (mttt) cc_final: 0.7191 (tttt) REVERT: E 189 ARG cc_start: 0.5941 (mmm-85) cc_final: 0.5568 (mmm-85) REVERT: E 256 SER cc_start: 0.9128 (p) cc_final: 0.8721 (t) REVERT: F 311 MET cc_start: 0.7525 (tpt) cc_final: 0.7069 (tpp) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.0809 time to fit residues: 9.3409 Evaluate side-chains 77 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 42 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116538 restraints weight = 8235.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119146 restraints weight = 5806.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120800 restraints weight = 4689.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121646 restraints weight = 4134.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121866 restraints weight = 3841.458| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6663 Z= 0.112 Angle : 0.659 9.843 9112 Z= 0.309 Chirality : 0.045 0.285 1064 Planarity : 0.003 0.027 1127 Dihedral : 11.049 86.789 1264 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.29 % Favored : 91.32 % Rotamer: Outliers : 1.72 % Allowed : 20.74 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: -0.00 (0.31), residues: 772 helix: -1.44 (0.75), residues: 43 sheet: 0.98 (0.27), residues: 345 loop : -0.74 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 289 TYR 0.010 0.001 TYR E 327 PHE 0.014 0.001 PHE F 329 TRP 0.008 0.001 TRP A 181 HIS 0.003 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6632) covalent geometry : angle 0.62406 ( 9029) SS BOND : bond 0.00252 ( 10) SS BOND : angle 0.56652 ( 20) hydrogen bonds : bond 0.02535 ( 221) hydrogen bonds : angle 4.19205 ( 633) link_ALPHA1-3 : bond 0.01576 ( 3) link_ALPHA1-3 : angle 3.33688 ( 9) link_ALPHA1-6 : bond 0.00722 ( 2) link_ALPHA1-6 : angle 1.57502 ( 6) link_BETA1-4 : bond 0.01220 ( 8) link_BETA1-4 : angle 2.86764 ( 24) link_BETA1-6 : bond 0.00225 ( 1) link_BETA1-6 : angle 1.28014 ( 3) link_NAG-ASN : bond 0.00137 ( 7) link_NAG-ASN : angle 2.32856 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.7896 (m-10) cc_final: 0.7667 (m-10) REVERT: E 183 LYS cc_start: 0.7565 (mttt) cc_final: 0.6998 (tttt) REVERT: F 311 MET cc_start: 0.7525 (tpt) cc_final: 0.7064 (tpp) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.0859 time to fit residues: 9.3502 Evaluate side-chains 77 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 chunk 12 optimal weight: 0.3980 chunk 35 optimal weight: 0.2980 chunk 36 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.161705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126692 restraints weight = 8098.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126113 restraints weight = 9512.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127752 restraints weight = 9028.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128227 restraints weight = 6199.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129142 restraints weight = 6074.260| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6663 Z= 0.112 Angle : 0.666 9.794 9112 Z= 0.313 Chirality : 0.045 0.280 1064 Planarity : 0.003 0.027 1127 Dihedral : 10.792 84.971 1264 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.42 % Favored : 91.19 % Rotamer: Outliers : 1.57 % Allowed : 21.03 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.07 (0.31), residues: 772 helix: -1.41 (0.76), residues: 43 sheet: 1.03 (0.27), residues: 345 loop : -0.69 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 289 TYR 0.009 0.001 TYR E 327 PHE 0.018 0.001 PHE E 329 TRP 0.008 0.001 TRP A 181 HIS 0.003 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6632) covalent geometry : angle 0.63092 ( 9029) SS BOND : bond 0.00218 ( 10) SS BOND : angle 0.56444 ( 20) hydrogen bonds : bond 0.02545 ( 221) hydrogen bonds : angle 4.16362 ( 633) link_ALPHA1-3 : bond 0.01590 ( 3) link_ALPHA1-3 : angle 3.36381 ( 9) link_ALPHA1-6 : bond 0.00708 ( 2) link_ALPHA1-6 : angle 1.58342 ( 6) link_BETA1-4 : bond 0.01217 ( 8) link_BETA1-4 : angle 2.85430 ( 24) link_BETA1-6 : bond 0.00239 ( 1) link_BETA1-6 : angle 1.27651 ( 3) link_NAG-ASN : bond 0.00126 ( 7) link_NAG-ASN : angle 2.36988 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.7773 (m-10) cc_final: 0.7557 (m-10) REVERT: E 183 LYS cc_start: 0.7581 (mttt) cc_final: 0.7169 (tttt) REVERT: F 306 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8443 (mp) REVERT: F 311 MET cc_start: 0.7414 (tpt) cc_final: 0.6966 (tpp) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.0804 time to fit residues: 8.5219 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 0.0770 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.160646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118391 restraints weight = 8170.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119425 restraints weight = 6506.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120049 restraints weight = 5475.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120135 restraints weight = 4890.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120245 restraints weight = 4946.327| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6663 Z= 0.132 Angle : 0.676 9.911 9112 Z= 0.318 Chirality : 0.045 0.275 1064 Planarity : 0.003 0.027 1127 Dihedral : 10.677 84.443 1264 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.68 % Favored : 90.93 % Rotamer: Outliers : 1.86 % Allowed : 20.74 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % 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 aren not related in a simple way. whole: 0.05 (0.31), residues: 772 helix: -1.39 (0.75), residues: 43 sheet: 1.00 (0.27), residues: 345 loop : -0.70 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 289 TYR 0.024 0.001 TYR E 327 PHE 0.017 0.001 PHE E 329 TRP 0.008 0.001 TRP A 181 HIS 0.004 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6632) covalent geometry : angle 0.64021 ( 9029) SS BOND : bond 0.00186 ( 10) SS BOND : angle 0.58054 ( 20) hydrogen bonds : bond 0.02656 ( 221) hydrogen bonds : angle 4.18509 ( 633) link_ALPHA1-3 : bond 0.01562 ( 3) link_ALPHA1-3 : angle 3.37263 ( 9) link_ALPHA1-6 : bond 0.00655 ( 2) link_ALPHA1-6 : angle 1.62320 ( 6) link_BETA1-4 : bond 0.01193 ( 8) link_BETA1-4 : angle 2.88289 ( 24) link_BETA1-6 : bond 0.00244 ( 1) link_BETA1-6 : angle 1.24549 ( 3) link_NAG-ASN : bond 0.00091 ( 7) link_NAG-ASN : angle 2.50420 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.63 seconds wall clock time: 22 minutes 33.95 seconds (1353.95 seconds total)