Starting phenix.real_space_refine on Fri Sep 11 11:11:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wv3_66281/09_2026/9wv3_66281.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wv3_66281/09_2026/9wv3_66281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wv3_66281/09_2026/9wv3_66281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wv3_66281/09_2026/9wv3_66281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wv3_66281/09_2026/9wv3_66281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wv3_66281/09_2026/9wv3_66281.map" } resolution = 2.98 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= 0.045 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: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 36 5.16 5 C 5832 2.51 5 N 1353 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8800 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "C" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "D" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "E" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "F" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 417 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "H" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 417 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "I" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "J" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2189 Classifications: {'peptide': 286} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "K" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 187 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "L" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 187 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'PC1': 1, 'R16': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'PC1': 1, 'R16': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Chain: "E" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PC1': 3, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PC1': 3, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "I" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 178 Unusual residues: {'PC1': 4, 'R16': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Chain: "J" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 178 Unusual residues: {'PC1': 4, 'R16': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8800 At special positions: 0 Unit cell: (114.95, 118.75, 95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 23 15.00 O 1556 8.00 N 1353 7.00 C 5832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 333.0 milliseconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 34.2% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 20 through 48 Proline residue: A 42 - end of helix Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 20 through 48 Proline residue: B 42 - end of helix Processing helix chain 'C' and resid 26 through 35 Processing helix chain 'C' and resid 40 through 60 Processing helix chain 'D' and resid 26 through 35 Processing helix chain 'D' and resid 40 through 60 Processing helix chain 'E' and resid 6 through 26 removed outlier: 3.511A pdb=" N PHE E 21 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'F' and resid 6 through 26 removed outlier: 3.500A pdb=" N PHE F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'G' and resid 72 through 96 removed outlier: 3.825A pdb=" N LYS G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 115 removed outlier: 3.825A pdb=" N GLU G 102 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 96 removed outlier: 3.797A pdb=" N LYS H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 115 removed outlier: 3.783A pdb=" N GLU H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 92 removed outlier: 3.575A pdb=" N LYS I 91 " --> pdb=" O HIS I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 92 removed outlier: 3.585A pdb=" N LYS J 91 " --> pdb=" O HIS J 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU J 92 " --> pdb=" O ARG J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 92' Processing helix chain 'K' and resid 263 through 274 removed outlier: 3.507A pdb=" N LYS K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) Proline residue: K 271 - end of helix Processing helix chain 'L' and resid 263 through 274 removed outlier: 3.990A pdb=" N GLY L 268 " --> pdb=" O ALA L 264 " (cutoff:3.500A) Proline residue: L 271 - end of helix Processing sheet with id=AA1, first strand: chain 'I' and resid 172 through 180 removed outlier: 3.796A pdb=" N VAL I 190 " --> pdb=" O LEU I 205 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 199 through 205 current: chain 'I' and resid 161 through 166 removed outlier: 5.687A pdb=" N GLY I 100 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU I 358 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL I 263 " --> pdb=" O GLY I 252 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS I 238 " --> pdb=" O GLY I 245 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA I 251 " --> pdb=" O GLY I 232 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY I 232 " --> pdb=" O ALA I 251 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU I 229 " --> pdb=" O ILE I 225 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE I 225 " --> pdb=" O LEU I 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 108 removed outlier: 3.984A pdb=" N LYS J 175 " --> pdb=" O ASP J 191 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL J 190 " --> pdb=" O LEU J 205 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE J 225 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU J 229 " --> pdb=" O ILE J 225 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY J 232 " --> pdb=" O ALA J 251 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA J 251 " --> pdb=" O GLY J 232 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL J 263 " --> pdb=" O GLY J 252 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY J 100 " --> pdb=" O CYS J 354 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1392 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: 1.16 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1374 1.32 - 1.45: 2177 1.45 - 1.57: 5278 1.57 - 1.69: 46 1.69 - 1.82: 62 Bond restraints: 8937 Sorted by residual: bond pdb=" CA VAL K 262 " pdb=" CB VAL K 262 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.01e+00 bond pdb=" CA THR K 270 " pdb=" C THR K 270 " ideal model delta sigma weight residual 1.520 1.530 -0.009 1.23e-02 6.61e+03 5.64e-01 bond pdb=" C LEU J 265 " pdb=" N GLY J 266 " ideal model delta sigma weight residual 1.331 1.320 0.011 1.46e-02 4.69e+03 5.56e-01 bond pdb=" N VAL L 262 " pdb=" CA VAL L 262 " ideal model delta sigma weight residual 1.474 1.463 0.011 1.57e-02 4.06e+03 5.14e-01 bond pdb=" C LEU I 265 " pdb=" N GLY I 266 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 5.09e-01 ... (remaining 8932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 11670 1.29 - 2.58: 168 2.58 - 3.88: 29 3.88 - 5.17: 14 5.17 - 6.46: 2 Bond angle restraints: 11883 Sorted by residual: angle pdb=" C LEU J 93 " pdb=" N PHE J 94 " pdb=" CA PHE J 94 " ideal model delta sigma weight residual 120.69 127.15 -6.46 2.95e+00 1.15e-01 4.80e+00 angle pdb=" CA CYS J 228 " pdb=" CB CYS J 228 " pdb=" SG CYS J 228 " ideal model delta sigma weight residual 114.40 119.36 -4.96 2.30e+00 1.89e-01 4.65e+00 angle pdb=" CA CYS I 228 " pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " ideal model delta sigma weight residual 114.40 119.35 -4.95 2.30e+00 1.89e-01 4.63e+00 angle pdb=" CA PRO I 170 " pdb=" CB PRO I 170 " pdb=" CG PRO I 170 " ideal model delta sigma weight residual 104.50 107.70 -3.20 1.90e+00 2.77e-01 2.83e+00 angle pdb=" CA PRO J 170 " pdb=" CB PRO J 170 " pdb=" CG PRO J 170 " ideal model delta sigma weight residual 104.50 107.60 -3.10 1.90e+00 2.77e-01 2.66e+00 ... (remaining 11878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4431 18.00 - 36.00: 727 36.00 - 54.00: 314 54.00 - 71.99: 91 71.99 - 89.99: 21 Dihedral angle restraints: 5584 sinusoidal: 2788 harmonic: 2796 Sorted by residual: dihedral pdb=" CA GLN I 181 " pdb=" C GLN I 181 " pdb=" N GLN I 182 " pdb=" CA GLN I 182 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLN J 181 " pdb=" C GLN J 181 " pdb=" N GLN J 182 " pdb=" CA GLN J 182 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ILE G 94 " pdb=" C ILE G 94 " pdb=" N LEU G 95 " pdb=" CA LEU G 95 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 692 0.025 - 0.049: 339 0.049 - 0.074: 101 0.074 - 0.098: 38 0.098 - 0.123: 53 Chirality restraints: 1223 Sorted by residual: chirality pdb=" CA ILE I 216 " pdb=" N ILE I 216 " pdb=" C ILE I 216 " pdb=" CB ILE I 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE J 216 " pdb=" N ILE J 216 " pdb=" C ILE J 216 " pdb=" CB ILE J 216 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA VAL I 324 " pdb=" N VAL I 324 " pdb=" C VAL I 324 " pdb=" CB VAL I 324 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1220 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 226 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO J 227 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO J 227 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 227 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 226 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO I 227 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO I 227 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 227 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 28 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO E 29 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.017 5.00e-02 4.00e+02 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2159 2.81 - 3.33: 6704 3.33 - 3.86: 12605 3.86 - 4.38: 14397 4.38 - 4.90: 28234 Nonbonded interactions: 64099 Sorted by model distance: nonbonded pdb=" OG SER I 159 " pdb=" O GLN I 181 " model vdw 2.289 3.040 nonbonded pdb=" O PHE K 266 " pdb=" OG1 THR K 270 " model vdw 2.289 3.040 nonbonded pdb=" O TYR D 32 " pdb=" OG1 THR D 36 " model vdw 2.295 3.040 nonbonded pdb=" O TYR C 32 " pdb=" OG1 THR C 36 " model vdw 2.298 3.040 nonbonded pdb=" NH2 ARG D 43 " pdb=" O12 PC1 J 401 " model vdw 2.313 3.120 ... (remaining 64094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 25 through 102 or (resid 103 and (name C29 or name C30 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or resid 104)) selection = (chain 'D' and (resid 25 through 101 or (resid 102 through 103 and (name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name C40 or name C41 or name C42)) or re \ sid 104)) } ncs_group { reference = (chain 'E' and (resid 5 through 101 or resid 104)) selection = (chain 'F' and (resid 5 through 101 or resid 104)) } ncs_group { reference = (chain 'G' and resid 68 through 201) selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 76 through 402 or (resid 404 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or n \ ame C3B or name C3C or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'J' and (resid 76 through 401 or (resid 402 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or n \ ame C3B or name C3C or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )) or resid 404)) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.020 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.002 0.024 8937 Z= 0.104 Angle : 0.441 6.462 11883 Z= 0.225 Chirality : 0.039 0.123 1223 Planarity : 0.003 0.038 1396 Dihedral : 21.299 89.993 3788 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.24 % Allowed : 30.22 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.29), residues: 962 helix: 2.65 (0.30), residues: 324 sheet: 0.40 (0.27), residues: 400 loop : -1.56 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 82 TYR 0.012 0.001 TYR H 78 PHE 0.014 0.001 PHE J 356 TRP 0.007 0.001 TRP J 259 HIS 0.002 0.001 HIS J 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 8937) covalent geometry : angle 0.44069 / 0.23 (11883) hydrogen bonds : bond 0.19666 / 13.03 ( 484) hydrogen bonds : angle 6.38458 / 4.75 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.238 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 25 residues processed: 85 average time/residue: 0.3984 time to fit residues: 36.9651 Evaluate side-chains 84 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain K residue 267 LYS Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain L residue 270 THR Chi-restraints excluded: chain L residue 281 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124502 restraints weight = 7947.860| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.41 r_work: 0.2927 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8937 Z= 0.190 Angle : 0.592 7.314 11883 Z= 0.299 Chirality : 0.043 0.142 1223 Planarity : 0.004 0.035 1396 Dihedral : 17.826 78.843 1982 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.32 % Allowed : 27.82 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.28), residues: 962 helix: 2.98 (0.30), residues: 314 sheet: 0.89 (0.27), residues: 382 loop : -1.31 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 82 TYR 0.013 0.001 TYR H 78 PHE 0.025 0.001 PHE J 356 TRP 0.011 0.001 TRP I 259 HIS 0.004 0.001 HIS J 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 ( 8937) covalent geometry : angle 0.59157 / 0.30 (11883) hydrogen bonds : bond 0.05165 / 3.42 ( 484) hydrogen bonds : angle 4.41727 / 3.26 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.309 Fit side-chains REVERT: E 44 MET cc_start: 0.7537 (mmm) cc_final: 0.7276 (mmm) REVERT: F 44 MET cc_start: 0.7383 (mmm) cc_final: 0.6223 (mtm) outliers start: 36 outliers final: 15 residues processed: 100 average time/residue: 0.5268 time to fit residues: 56.7078 Evaluate side-chains 71 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.199298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126794 restraints weight = 7983.081| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.44 r_work: 0.3182 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8937 Z= 0.107 Angle : 0.494 6.795 11883 Z= 0.251 Chirality : 0.040 0.134 1223 Planarity : 0.003 0.037 1396 Dihedral : 17.078 78.710 1962 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.48 % Allowed : 28.54 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.28), residues: 962 helix: 3.15 (0.29), residues: 314 sheet: 1.23 (0.27), residues: 382 loop : -1.26 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 82 TYR 0.011 0.001 TYR H 78 PHE 0.019 0.001 PHE J 356 TRP 0.008 0.001 TRP J 259 HIS 0.003 0.001 HIS J 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8937) covalent geometry : angle 0.49382 / 0.25 (11883) hydrogen bonds : bond 0.03840 / 2.55 ( 484) hydrogen bonds : angle 4.08155 / 3.00 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.322 Fit side-chains REVERT: A 19 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7836 (ttpt) REVERT: E 44 MET cc_start: 0.7582 (mmm) cc_final: 0.7363 (mmm) REVERT: I 96 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8438 (pp) REVERT: I 182 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: J 182 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7844 (mt0) outliers start: 29 outliers final: 8 residues processed: 87 average time/residue: 0.4895 time to fit residues: 46.0748 Evaluate side-chains 73 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 0.0030 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.200022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127260 restraints weight = 8076.653| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.47 r_work: 0.3301 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8937 Z= 0.102 Angle : 0.480 7.961 11883 Z= 0.242 Chirality : 0.039 0.133 1223 Planarity : 0.003 0.039 1396 Dihedral : 16.562 78.852 1954 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.48 % Allowed : 28.66 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.29), residues: 962 helix: 3.16 (0.30), residues: 316 sheet: 1.36 (0.27), residues: 384 loop : -1.16 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 82 TYR 0.011 0.001 TYR H 78 PHE 0.018 0.001 PHE J 356 TRP 0.007 0.001 TRP I 259 HIS 0.002 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 8937) covalent geometry : angle 0.48035 / 0.24 (11883) hydrogen bonds : bond 0.03478 / 2.30 ( 484) hydrogen bonds : angle 3.86213 / 2.83 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.308 Fit side-chains REVERT: A 19 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7853 (ttpt) REVERT: B 45 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6811 (mp) REVERT: F 44 MET cc_start: 0.7176 (mmm) cc_final: 0.5650 (mtm) REVERT: H 102 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7715 (mm-30) REVERT: I 96 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8403 (pp) REVERT: I 182 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7818 (mt0) REVERT: J 96 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8455 (pp) REVERT: J 182 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7804 (mt0) outliers start: 29 outliers final: 10 residues processed: 90 average time/residue: 0.4795 time to fit residues: 46.8255 Evaluate side-chains 81 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.199334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126716 restraints weight = 8020.853| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.44 r_work: 0.3136 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8937 Z= 0.117 Angle : 0.506 9.370 11883 Z= 0.252 Chirality : 0.040 0.131 1223 Planarity : 0.003 0.039 1396 Dihedral : 16.371 79.451 1950 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.48 % Allowed : 29.26 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.28), residues: 962 helix: 3.15 (0.29), residues: 316 sheet: 1.38 (0.27), residues: 384 loop : -1.11 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 82 TYR 0.011 0.001 TYR H 78 PHE 0.021 0.001 PHE J 356 TRP 0.008 0.001 TRP J 259 HIS 0.002 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8937) covalent geometry : angle 0.50596 / 0.25 (11883) hydrogen bonds : bond 0.03685 / 2.44 ( 484) hydrogen bonds : angle 3.85083 / 2.82 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.265 Fit side-chains REVERT: A 19 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7883 (ttpt) REVERT: B 45 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6906 (mp) REVERT: E 44 MET cc_start: 0.7396 (mmm) cc_final: 0.6180 (mtm) REVERT: F 44 MET cc_start: 0.7166 (mmm) cc_final: 0.5734 (mtm) REVERT: H 102 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7755 (mm-30) REVERT: H 108 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6749 (ttp) REVERT: I 96 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8471 (pp) REVERT: I 182 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: J 96 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8516 (pp) REVERT: J 182 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7855 (mt0) outliers start: 29 outliers final: 13 residues processed: 90 average time/residue: 0.4503 time to fit residues: 44.0230 Evaluate side-chains 85 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.198992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126454 restraints weight = 8009.242| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.44 r_work: 0.3125 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8937 Z= 0.119 Angle : 0.501 9.165 11883 Z= 0.251 Chirality : 0.040 0.130 1223 Planarity : 0.003 0.039 1396 Dihedral : 16.146 79.937 1948 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.24 % Allowed : 29.86 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.29), residues: 962 helix: 3.15 (0.29), residues: 316 sheet: 1.40 (0.27), residues: 384 loop : -1.08 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 38 TYR 0.011 0.001 TYR H 78 PHE 0.021 0.001 PHE J 356 TRP 0.008 0.001 TRP I 259 HIS 0.002 0.001 HIS J 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 8937) covalent geometry : angle 0.50075 / 0.25 (11883) hydrogen bonds : bond 0.03688 / 2.44 ( 484) hydrogen bonds : angle 3.81696 / 2.79 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.339 Fit side-chains REVERT: A 19 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7884 (ttpt) REVERT: B 45 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6903 (mp) REVERT: E 44 MET cc_start: 0.7296 (mmm) cc_final: 0.6005 (mtm) REVERT: H 108 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6814 (ttp) REVERT: I 96 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8468 (pp) REVERT: I 182 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: J 96 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8509 (pp) REVERT: J 182 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7846 (mt0) outliers start: 27 outliers final: 14 residues processed: 85 average time/residue: 0.4484 time to fit residues: 41.5086 Evaluate side-chains 85 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain J residue 317 SER Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.197993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124911 restraints weight = 8083.115| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.48 r_work: 0.3054 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8937 Z= 0.141 Angle : 0.542 12.303 11883 Z= 0.268 Chirality : 0.041 0.130 1223 Planarity : 0.003 0.038 1396 Dihedral : 16.215 80.468 1948 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.36 % Allowed : 30.10 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.28), residues: 962 helix: 3.10 (0.29), residues: 316 sheet: 1.37 (0.27), residues: 384 loop : -1.09 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 43 TYR 0.011 0.001 TYR H 78 PHE 0.023 0.001 PHE J 356 TRP 0.008 0.001 TRP J 259 HIS 0.003 0.001 HIS I 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 ( 8937) covalent geometry : angle 0.54178 / 0.27 (11883) hydrogen bonds : bond 0.04013 / 2.66 ( 484) hydrogen bonds : angle 3.84760 / 2.81 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 45 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6887 (mp) REVERT: E 44 MET cc_start: 0.7285 (mmm) cc_final: 0.5966 (mtm) REVERT: H 108 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6815 (ttp) REVERT: I 96 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8448 (pp) REVERT: I 182 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: J 96 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8484 (pp) REVERT: J 182 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7860 (mt0) outliers start: 28 outliers final: 12 residues processed: 83 average time/residue: 0.4371 time to fit residues: 39.5804 Evaluate side-chains 79 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.196231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123435 restraints weight = 8046.895| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.44 r_work: 0.3085 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8937 Z= 0.189 Angle : 0.589 10.515 11883 Z= 0.292 Chirality : 0.043 0.132 1223 Planarity : 0.004 0.035 1396 Dihedral : 16.606 81.931 1948 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.36 % Allowed : 29.98 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.29), residues: 962 helix: 3.10 (0.30), residues: 314 sheet: 1.28 (0.27), residues: 384 loop : -1.20 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 43 TYR 0.012 0.001 TYR H 78 PHE 0.026 0.001 PHE J 356 TRP 0.009 0.001 TRP J 259 HIS 0.003 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.19 ( 8937) covalent geometry : angle 0.58890 / 0.29 (11883) hydrogen bonds : bond 0.04564 / 3.02 ( 484) hydrogen bonds : angle 3.92103 / 2.86 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 45 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7005 (mp) REVERT: H 108 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6919 (ttp) REVERT: I 96 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8544 (pp) REVERT: J 96 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8496 (pp) REVERT: J 182 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7941 (mt0) outliers start: 28 outliers final: 12 residues processed: 82 average time/residue: 0.4738 time to fit residues: 42.2233 Evaluate side-chains 74 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.199898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127513 restraints weight = 8000.669| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.45 r_work: 0.3246 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8937 Z= 0.101 Angle : 0.517 15.154 11883 Z= 0.252 Chirality : 0.040 0.126 1223 Planarity : 0.003 0.037 1396 Dihedral : 15.986 81.242 1948 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.28 % Allowed : 30.94 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 962 helix: 3.11 (0.30), residues: 316 sheet: 1.37 (0.27), residues: 384 loop : -1.07 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 82 TYR 0.010 0.001 TYR H 78 PHE 0.019 0.001 PHE J 356 TRP 0.008 0.001 TRP J 259 HIS 0.002 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 8937) covalent geometry : angle 0.51737 / 0.25 (11883) hydrogen bonds : bond 0.03382 / 2.25 ( 484) hydrogen bonds : angle 3.78130 / 2.76 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6838 (mp) REVERT: H 108 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6714 (ttp) REVERT: I 96 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8469 (pp) REVERT: J 182 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7866 (mt0) outliers start: 19 outliers final: 12 residues processed: 80 average time/residue: 0.4336 time to fit residues: 37.9864 Evaluate side-chains 81 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.197561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124836 restraints weight = 8003.547| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.44 r_work: 0.3110 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8937 Z= 0.153 Angle : 0.569 13.981 11883 Z= 0.277 Chirality : 0.041 0.128 1223 Planarity : 0.003 0.037 1396 Dihedral : 16.225 81.016 1948 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.92 % Allowed : 31.29 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.28), residues: 962 helix: 3.06 (0.30), residues: 316 sheet: 1.37 (0.27), residues: 382 loop : -1.02 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 43 TYR 0.012 0.001 TYR H 78 PHE 0.024 0.001 PHE J 356 TRP 0.009 0.001 TRP J 259 HIS 0.003 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.15 ( 8937) covalent geometry : angle 0.56883 / 0.28 (11883) hydrogen bonds : bond 0.04130 / 2.73 ( 484) hydrogen bonds : angle 3.83123 / 2.79 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6871 (mp) REVERT: H 108 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6844 (ttp) REVERT: I 96 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8531 (pp) REVERT: J 182 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7895 (mt0) outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 0.4948 time to fit residues: 38.6942 Evaluate side-chains 73 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 297 THR Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.202939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130089 restraints weight = 7916.494| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.40 r_work: 0.3193 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8937 Z= 0.115 Angle : 0.531 13.385 11883 Z= 0.259 Chirality : 0.040 0.126 1223 Planarity : 0.003 0.037 1396 Dihedral : 15.976 80.967 1948 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.16 % Allowed : 30.94 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.29), residues: 962 helix: 3.11 (0.29), residues: 316 sheet: 1.38 (0.27), residues: 384 loop : -1.01 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 82 TYR 0.011 0.001 TYR H 78 PHE 0.020 0.001 PHE J 356 TRP 0.008 0.001 TRP J 259 HIS 0.002 0.001 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.11 ( 8937) covalent geometry : angle 0.53051 / 0.26 (11883) hydrogen bonds : bond 0.03610 / 2.40 ( 484) hydrogen bonds : angle 3.77731 / 2.75 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.77 seconds wall clock time: 45 minutes 40.76 seconds (2740.76 seconds total)