Starting phenix.real_space_refine on Sun Apr 27 19:11:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7r_36939/04_2025/8k7r_36939.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7r_36939/04_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_36939/04_2025/8k7r_36939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7r_36939/04_2025/8k7r_36939.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7r_36939/04_2025/8k7r_36939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7r_36939/04_2025/8k7r_36939.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.06, per 1000 atoms: 0.63 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: 2.07 Conformation dependent library (CDL) restraints added in 788.8 milliseconds 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: 0.87 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: 1.85 Time building geometry restraints manager: 2.27 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.650 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 181 HIS 0.008 0.001 HIS A 95 PHE 0.016 0.001 PHE E 329 TYR 0.006 0.001 TYR A 175 ARG 0.004 0.000 ARG E 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 7) link_NAG-ASN : angle 1.81628 ( 21) 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_ALPHA1-3 : bond 0.00907 ( 3) link_ALPHA1-3 : angle 2.65000 ( 9) hydrogen bonds : bond 0.10931 ( 221) hydrogen bonds : angle 5.43966 ( 633) link_BETA1-6 : bond 0.00362 ( 1) link_BETA1-6 : angle 1.30001 ( 3) SS BOND : bond 0.00246 ( 10) SS BOND : angle 0.68021 ( 20) covalent geometry : bond 0.00552 ( 6632) covalent geometry : angle 0.77454 ( 9029) *********************** 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 : 0.736 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: 0.1939 time to fit residues: 20.5243 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 : 0.760 ------------------------------------------------------------------------------- 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 65 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.160808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.114819 restraints weight = 8154.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117068 restraints weight = 6095.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117770 restraints weight = 4794.182| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6663 Z= 0.180 Angle : 0.677 9.511 9112 Z= 0.319 Chirality : 0.047 0.267 1064 Planarity : 0.005 0.047 1127 Dihedral : 16.118 106.436 1269 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.32 % Rotamer: Outliers : 2.58 % Allowed : 19.46 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.31), residues: 772 helix: -0.96 (0.78), residues: 43 sheet: 1.16 (0.27), residues: 349 loop : -0.92 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 38 HIS 0.008 0.001 HIS A 95 PHE 0.008 0.001 PHE E 329 TYR 0.015 0.001 TYR E 327 ARG 0.005 0.000 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 7) link_NAG-ASN : angle 2.44706 ( 21) link_ALPHA1-6 : bond 0.00915 ( 2) link_ALPHA1-6 : angle 1.40278 ( 6) link_BETA1-4 : bond 0.01255 ( 8) link_BETA1-4 : angle 2.83267 ( 24) link_ALPHA1-3 : bond 0.01317 ( 3) link_ALPHA1-3 : angle 3.37029 ( 9) hydrogen bonds : bond 0.03258 ( 221) hydrogen bonds : angle 4.63553 ( 633) link_BETA1-6 : bond 0.00438 ( 1) link_BETA1-6 : angle 1.37725 ( 3) SS BOND : bond 0.00208 ( 10) SS BOND : angle 0.89320 ( 20) covalent geometry : bond 0.00430 ( 6632) covalent geometry : angle 0.64249 ( 9029) *********************** 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 98 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7319 (tp30) cc_final: 0.6990 (tp30) REVERT: E 311 MET cc_start: 0.6964 (tpp) cc_final: 0.6751 (tpt) outliers start: 18 outliers final: 6 residues processed: 94 average time/residue: 0.1813 time to fit residues: 23.1235 Evaluate side-chains 80 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 202 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 52 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** 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 = 0.3770 r_free = 0.3770 target = 0.162839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127445 restraints weight = 8128.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122556 restraints weight = 9925.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.123991 restraints weight = 12936.647| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1111 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= 0.130 Angle : 0.643 9.752 9112 Z= 0.302 Chirality : 0.045 0.250 1064 Planarity : 0.004 0.035 1127 Dihedral : 14.984 104.048 1264 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.42 % Favored : 91.19 % Rotamer: Outliers : 2.00 % Allowed : 18.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.30), residues: 772 helix: -1.12 (0.78), residues: 42 sheet: 1.16 (0.27), residues: 349 loop : -0.88 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 291 HIS 0.008 0.001 HIS A 95 PHE 0.014 0.001 PHE E 329 TYR 0.019 0.001 TYR F 197 ARG 0.003 0.000 ARG E 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 7) link_NAG-ASN : angle 2.19586 ( 21) link_ALPHA1-6 : bond 0.01035 ( 2) link_ALPHA1-6 : angle 1.49929 ( 6) link_BETA1-4 : bond 0.01190 ( 8) link_BETA1-4 : angle 2.72775 ( 24) link_ALPHA1-3 : bond 0.01471 ( 3) link_ALPHA1-3 : angle 3.14751 ( 9) hydrogen bonds : bond 0.02880 ( 221) hydrogen bonds : angle 4.47879 ( 633) link_BETA1-6 : bond 0.00178 ( 1) link_BETA1-6 : angle 1.18319 ( 3) SS BOND : bond 0.00165 ( 10) SS BOND : angle 0.56359 ( 20) covalent geometry : bond 0.00288 ( 6632) covalent geometry : angle 0.61126 ( 9029) *********************** 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 91 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 MET cc_start: 0.7202 (tpp) cc_final: 0.6819 (tpt) REVERT: F 306 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8345 (mp) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 0.1815 time to fit residues: 21.9535 Evaluate side-chains 81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 E residue 269 LYS Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 306 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.161378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116256 restraints weight = 8251.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.118154 restraints weight = 6052.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118660 restraints weight = 4873.635| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1395 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= 0.141 Angle : 0.661 10.068 9112 Z= 0.310 Chirality : 0.046 0.266 1064 Planarity : 0.004 0.047 1127 Dihedral : 13.843 100.547 1264 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.03 % Favored : 91.71 % Rotamer: Outliers : 2.86 % Allowed : 18.31 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.30), residues: 772 helix: -1.18 (0.77), residues: 42 sheet: 1.14 (0.27), residues: 347 loop : -0.87 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 38 HIS 0.006 0.001 HIS A 95 PHE 0.008 0.001 PHE E 329 TYR 0.016 0.001 TYR E 327 ARG 0.006 0.000 ARG F 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 7) link_NAG-ASN : angle 2.23256 ( 21) link_ALPHA1-6 : bond 0.01097 ( 2) link_ALPHA1-6 : angle 1.52251 ( 6) link_BETA1-4 : bond 0.01221 ( 8) link_BETA1-4 : angle 2.82141 ( 24) link_ALPHA1-3 : bond 0.01467 ( 3) link_ALPHA1-3 : angle 3.20865 ( 9) hydrogen bonds : bond 0.02805 ( 221) hydrogen bonds : angle 4.40458 ( 633) link_BETA1-6 : bond 0.00281 ( 1) link_BETA1-6 : angle 1.26641 ( 3) SS BOND : bond 0.00171 ( 10) SS BOND : angle 0.74772 ( 20) covalent geometry : bond 0.00321 ( 6632) covalent geometry : angle 0.62821 ( 9029) *********************** 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 95 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: E 183 LYS cc_start: 0.7329 (mttt) cc_final: 0.6872 (tttt) REVERT: E 189 ARG cc_start: 0.6382 (mmm-85) cc_final: 0.5947 (mmm-85) REVERT: E 264 ASN cc_start: 0.8182 (m-40) cc_final: 0.7921 (m110) REVERT: E 311 MET cc_start: 0.7119 (tpp) cc_final: 0.6748 (tpt) REVERT: F 306 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8546 (mp) outliers start: 20 outliers final: 11 residues processed: 93 average time/residue: 0.1986 time to fit residues: 25.2366 Evaluate side-chains 85 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 A residue 177 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 278 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 317 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS F 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.161468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.115197 restraints weight = 8209.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117499 restraints weight = 6114.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118790 restraints weight = 5129.188| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1621 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= 0.140 Angle : 0.656 9.812 9112 Z= 0.305 Chirality : 0.046 0.285 1064 Planarity : 0.003 0.031 1127 Dihedral : 12.851 98.229 1264 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.32 % Rotamer: Outliers : 2.43 % Allowed : 19.17 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.30), residues: 772 helix: -1.25 (0.76), residues: 42 sheet: 1.12 (0.27), residues: 344 loop : -0.85 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 291 HIS 0.004 0.001 HIS A 95 PHE 0.008 0.001 PHE E 387 TYR 0.008 0.001 TYR A 174 ARG 0.003 0.000 ARG E 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 7) link_NAG-ASN : angle 2.33838 ( 21) link_ALPHA1-6 : bond 0.00980 ( 2) link_ALPHA1-6 : angle 2.19587 ( 6) link_BETA1-4 : bond 0.01195 ( 8) link_BETA1-4 : angle 2.82189 ( 24) link_ALPHA1-3 : bond 0.01494 ( 3) link_ALPHA1-3 : angle 3.26944 ( 9) hydrogen bonds : bond 0.02765 ( 221) hydrogen bonds : angle 4.35966 ( 633) link_BETA1-6 : bond 0.00233 ( 1) link_BETA1-6 : angle 1.27850 ( 3) SS BOND : bond 0.00198 ( 10) SS BOND : angle 0.70906 ( 20) covalent geometry : bond 0.00318 ( 6632) covalent geometry : angle 0.62014 ( 9029) *********************** 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 91 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6996 (ttpt) cc_final: 0.6774 (ttpt) REVERT: A 131 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: E 183 LYS cc_start: 0.7476 (mttt) cc_final: 0.6994 (tttt) REVERT: E 264 ASN cc_start: 0.8182 (m-40) cc_final: 0.7917 (m110) REVERT: E 311 MET cc_start: 0.6997 (tpp) cc_final: 0.6630 (tpt) outliers start: 17 outliers final: 8 residues processed: 89 average time/residue: 0.2558 time to fit residues: 31.5827 Evaluate side-chains 79 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 392 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.160104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.114408 restraints weight = 8230.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117041 restraints weight = 6168.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117446 restraints weight = 4757.170| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1757 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= 0.147 Angle : 0.669 10.110 9112 Z= 0.315 Chirality : 0.046 0.292 1064 Planarity : 0.004 0.028 1127 Dihedral : 12.411 96.548 1264 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.16 % Favored : 91.58 % Rotamer: Outliers : 2.43 % Allowed : 19.31 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.31), residues: 772 helix: -1.34 (0.76), residues: 42 sheet: 1.10 (0.27), residues: 352 loop : -0.83 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 38 HIS 0.003 0.001 HIS A 95 PHE 0.021 0.002 PHE E 329 TYR 0.008 0.001 TYR E 327 ARG 0.004 0.000 ARG F 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 7) link_NAG-ASN : angle 2.34181 ( 21) link_ALPHA1-6 : bond 0.00724 ( 2) link_ALPHA1-6 : angle 1.91876 ( 6) link_BETA1-4 : bond 0.01184 ( 8) link_BETA1-4 : angle 2.93512 ( 24) link_ALPHA1-3 : bond 0.01451 ( 3) link_ALPHA1-3 : angle 3.34391 ( 9) hydrogen bonds : bond 0.02789 ( 221) hydrogen bonds : angle 4.35997 ( 633) link_BETA1-6 : bond 0.00224 ( 1) link_BETA1-6 : angle 1.29373 ( 3) SS BOND : bond 0.00180 ( 10) SS BOND : angle 0.62096 ( 20) covalent geometry : bond 0.00338 ( 6632) covalent geometry : angle 0.63320 ( 9029) *********************** 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 87 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7026 (ttpt) cc_final: 0.6818 (ttpt) REVERT: A 131 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7951 (ttt180) REVERT: E 183 LYS cc_start: 0.7616 (mttt) cc_final: 0.7201 (tttt) REVERT: E 256 SER cc_start: 0.9059 (p) cc_final: 0.8710 (t) REVERT: E 264 ASN cc_start: 0.8204 (m-40) cc_final: 0.7933 (m110) REVERT: F 306 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8551 (mp) outliers start: 17 outliers final: 9 residues processed: 85 average time/residue: 0.3027 time to fit residues: 36.7659 Evaluate side-chains 79 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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 306 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 49 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.160152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.115018 restraints weight = 8101.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.117357 restraints weight = 5763.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119018 restraints weight = 4695.619| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1820 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= 0.125 Angle : 0.649 9.985 9112 Z= 0.303 Chirality : 0.045 0.292 1064 Planarity : 0.003 0.027 1127 Dihedral : 11.938 93.898 1264 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.32 % Rotamer: Outliers : 1.86 % Allowed : 20.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.31), residues: 772 helix: -1.44 (0.75), residues: 43 sheet: 1.05 (0.27), residues: 354 loop : -0.78 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 291 HIS 0.003 0.000 HIS A 95 PHE 0.015 0.001 PHE E 329 TYR 0.007 0.001 TYR A 174 ARG 0.003 0.000 ARG F 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 7) link_NAG-ASN : angle 2.32199 ( 21) link_ALPHA1-6 : bond 0.00698 ( 2) link_ALPHA1-6 : angle 1.74451 ( 6) link_BETA1-4 : bond 0.01196 ( 8) link_BETA1-4 : angle 2.89796 ( 24) link_ALPHA1-3 : bond 0.01432 ( 3) link_ALPHA1-3 : angle 3.25268 ( 9) hydrogen bonds : bond 0.02658 ( 221) hydrogen bonds : angle 4.28059 ( 633) link_BETA1-6 : bond 0.00186 ( 1) link_BETA1-6 : angle 1.28389 ( 3) SS BOND : bond 0.00188 ( 10) SS BOND : angle 0.59072 ( 20) covalent geometry : bond 0.00278 ( 6632) covalent geometry : angle 0.61296 ( 9029) *********************** 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 83 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7529 (tt0) cc_final: 0.7313 (tt0) REVERT: A 131 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8008 (ttt180) REVERT: E 183 LYS cc_start: 0.7491 (mttt) cc_final: 0.6982 (tttt) REVERT: F 306 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8532 (mp) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.4053 time to fit residues: 45.1279 Evaluate side-chains 79 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 177 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 E residue 401 ASP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 306 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 50 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.158504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115889 restraints weight = 8152.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117448 restraints weight = 6539.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117888 restraints weight = 5371.690| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6663 Z= 0.151 Angle : 0.670 10.185 9112 Z= 0.315 Chirality : 0.046 0.293 1064 Planarity : 0.003 0.027 1127 Dihedral : 11.789 95.700 1264 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.42 % Favored : 91.32 % Rotamer: Outliers : 1.86 % Allowed : 20.46 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.31), residues: 772 helix: -1.47 (0.75), residues: 43 sheet: 1.06 (0.27), residues: 352 loop : -0.81 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 38 HIS 0.003 0.001 HIS A 95 PHE 0.015 0.001 PHE E 329 TYR 0.008 0.001 TYR A 174 ARG 0.003 0.000 ARG F 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 7) link_NAG-ASN : angle 2.43072 ( 21) link_ALPHA1-6 : bond 0.00618 ( 2) link_ALPHA1-6 : angle 1.77565 ( 6) link_BETA1-4 : bond 0.01190 ( 8) link_BETA1-4 : angle 2.97414 ( 24) link_ALPHA1-3 : bond 0.01395 ( 3) link_ALPHA1-3 : angle 3.23230 ( 9) hydrogen bonds : bond 0.02760 ( 221) hydrogen bonds : angle 4.29099 ( 633) link_BETA1-6 : bond 0.00193 ( 1) link_BETA1-6 : angle 1.30573 ( 3) SS BOND : bond 0.00159 ( 10) SS BOND : angle 0.63482 ( 20) covalent geometry : bond 0.00348 ( 6632) covalent geometry : angle 0.63379 ( 9029) *********************** 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 84 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7639 (tt0) cc_final: 0.7426 (tt0) REVERT: A 131 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7900 (ttt180) REVERT: E 183 LYS cc_start: 0.7638 (mttt) cc_final: 0.7227 (tttt) REVERT: E 256 SER cc_start: 0.9097 (p) cc_final: 0.8747 (t) REVERT: F 306 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8547 (mp) REVERT: F 311 MET cc_start: 0.7548 (tpt) cc_final: 0.7098 (tpp) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.2473 time to fit residues: 27.8287 Evaluate side-chains 82 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 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 284 LEU Chi-restraints excluded: chain F residue 306 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 16 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.152732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109406 restraints weight = 8344.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.111286 restraints weight = 6429.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.111313 restraints weight = 5122.401| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 6663 Z= 0.299 Angle : 0.781 11.202 9112 Z= 0.374 Chirality : 0.050 0.294 1064 Planarity : 0.005 0.039 1127 Dihedral : 12.543 104.924 1264 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.72 % Favored : 90.03 % Rotamer: Outliers : 2.15 % Allowed : 20.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.30), residues: 772 helix: -1.46 (0.74), residues: 43 sheet: 0.80 (0.27), residues: 352 loop : -1.07 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 38 HIS 0.004 0.001 HIS A 133 PHE 0.023 0.003 PHE E 329 TYR 0.012 0.002 TYR E 327 ARG 0.008 0.001 ARG F 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 7) link_NAG-ASN : angle 2.92573 ( 21) link_ALPHA1-6 : bond 0.00503 ( 2) link_ALPHA1-6 : angle 1.92349 ( 6) link_BETA1-4 : bond 0.01238 ( 8) link_BETA1-4 : angle 3.36311 ( 24) link_ALPHA1-3 : bond 0.01161 ( 3) link_ALPHA1-3 : angle 3.18637 ( 9) hydrogen bonds : bond 0.03504 ( 221) hydrogen bonds : angle 4.74913 ( 633) link_BETA1-6 : bond 0.00204 ( 1) link_BETA1-6 : angle 1.43535 ( 3) SS BOND : bond 0.00428 ( 10) SS BOND : angle 1.12663 ( 20) covalent geometry : bond 0.00721 ( 6632) covalent geometry : angle 0.74151 ( 9029) *********************** 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 88 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8515 (ttt180) REVERT: E 183 LYS cc_start: 0.7923 (mttt) cc_final: 0.7412 (tttt) REVERT: E 256 SER cc_start: 0.9101 (p) cc_final: 0.8778 (t) REVERT: E 264 ASN cc_start: 0.8293 (m-40) cc_final: 0.8039 (m110) REVERT: F 311 MET cc_start: 0.7650 (tpt) cc_final: 0.7184 (tpp) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.2580 time to fit residues: 31.0038 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 : 0.799 ------------------------------------------------------------------------------- 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 A residue 177 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS F 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.113326 restraints weight = 8291.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115337 restraints weight = 6259.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.116617 restraints weight = 5293.604| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2345 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 : 0.702 10.634 9112 Z= 0.335 Chirality : 0.046 0.277 1064 Planarity : 0.004 0.031 1127 Dihedral : 11.872 101.554 1264 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.68 % Favored : 91.06 % Rotamer: Outliers : 1.14 % Allowed : 21.75 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 772 helix: -1.42 (0.74), residues: 43 sheet: 0.92 (0.27), residues: 350 loop : -0.93 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 291 HIS 0.003 0.001 HIS A 95 PHE 0.023 0.002 PHE E 329 TYR 0.009 0.001 TYR A 174 ARG 0.007 0.000 ARG F 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 7) link_NAG-ASN : angle 2.49880 ( 21) link_ALPHA1-6 : bond 0.00606 ( 2) link_ALPHA1-6 : angle 1.55257 ( 6) link_BETA1-4 : bond 0.01227 ( 8) link_BETA1-4 : angle 3.03647 ( 24) link_ALPHA1-3 : bond 0.01417 ( 3) link_ALPHA1-3 : angle 3.24882 ( 9) hydrogen bonds : bond 0.02749 ( 221) hydrogen bonds : angle 4.51349 ( 633) link_BETA1-6 : bond 0.00071 ( 1) link_BETA1-6 : angle 1.45379 ( 3) SS BOND : bond 0.00300 ( 10) SS BOND : angle 0.61402 ( 20) covalent geometry : bond 0.00295 ( 6632) covalent geometry : angle 0.66687 ( 9029) ********************** 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 81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7949 (ttp-170) REVERT: E 183 LYS cc_start: 0.7730 (mttt) cc_final: 0.7280 (tttt) REVERT: E 256 SER cc_start: 0.9131 (p) cc_final: 0.8802 (t) REVERT: E 264 ASN cc_start: 0.8184 (m-40) cc_final: 0.7889 (m110) REVERT: E 329 PHE cc_start: 0.5338 (p90) cc_final: 0.5004 (p90) REVERT: F 311 MET cc_start: 0.7607 (tpt) cc_final: 0.7150 (tpp) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.2122 time to fit residues: 22.7981 Evaluate side-chains 76 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 278 LEU Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain F residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.158791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116397 restraints weight = 8289.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118330 restraints weight = 6302.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118531 restraints weight = 5054.974| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6663 Z= 0.124 Angle : 0.698 10.692 9112 Z= 0.330 Chirality : 0.046 0.271 1064 Planarity : 0.004 0.031 1127 Dihedral : 11.480 98.857 1264 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.68 % Favored : 91.06 % Rotamer: Outliers : 1.00 % Allowed : 22.17 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.31), residues: 772 helix: -1.57 (0.74), residues: 43 sheet: 0.90 (0.27), residues: 352 loop : -0.84 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 291 HIS 0.003 0.000 HIS A 95 PHE 0.021 0.001 PHE E 329 TYR 0.008 0.001 TYR A 174 ARG 0.007 0.000 ARG F 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 7) link_NAG-ASN : angle 2.43149 ( 21) link_ALPHA1-6 : bond 0.00677 ( 2) link_ALPHA1-6 : angle 1.57599 ( 6) link_BETA1-4 : bond 0.01283 ( 8) link_BETA1-4 : angle 3.02473 ( 24) link_ALPHA1-3 : bond 0.01397 ( 3) link_ALPHA1-3 : angle 3.16283 ( 9) hydrogen bonds : bond 0.02650 ( 221) hydrogen bonds : angle 4.42373 ( 633) link_BETA1-6 : bond 0.00146 ( 1) link_BETA1-6 : angle 1.36798 ( 3) SS BOND : bond 0.00198 ( 10) SS BOND : angle 0.56263 ( 20) covalent geometry : bond 0.00269 ( 6632) covalent geometry : angle 0.66369 ( 9029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.25 seconds wall clock time: 57 minutes 39.99 seconds (3459.99 seconds total)