Starting phenix.real_space_refine on Wed Mar 4 00:19:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vd2_31904/03_2026/7vd2_31904_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vd2_31904/03_2026/7vd2_31904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2026/7vd2_31904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2026/7vd2_31904.map" model { file = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2026/7vd2_31904_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vd2_31904/03_2026/7vd2_31904_neut.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 27 5.49 5 S 34 5.16 5 C 6179 2.51 5 N 1322 2.21 5 O 1555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9117 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "D" 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: "F" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 354 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" 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: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 463 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "J" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "B" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2190 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "I" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2190 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 272} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'PC1': 2, 'UND': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'PC1': 1, 'UND': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 227 Unusual residues: {'PC1': 4, 'UND': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'PC1': 3, 'UND': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'PC1': 2, 'UND': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 227 Unusual residues: {'PC1': 4, 'UND': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 314 Unusual residues: {'PC1': 5, 'UND': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 368 Unusual residues: {'PC1': 6, 'UND': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 2.23, per 1000 atoms: 0.24 Number of scatterers: 9117 At special positions: 0 Unit cell: (132.398, 113.845, 95.2929, 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 34 16.00 P 27 15.00 O 1555 8.00 N 1322 7.00 C 6179 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: 0.93 Conformation dependent library (CDL) restraints added in 296.7 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 37.5% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.596A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 60 Processing helix chain 'D' and resid 14 through 48 Proline residue: D 42 - end of helix Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.506A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 61 Processing helix chain 'G' and resid 5 through 39 removed outlier: 3.914A pdb=" N GLN G 10 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'E' and resid 16 through 48 removed outlier: 3.553A pdb=" N MET E 20 " --> pdb=" O MET E 16 " (cutoff:3.500A) Proline residue: E 42 - end of helix Processing helix chain 'H' and resid 64 through 96 removed outlier: 3.871A pdb=" N ASP H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 118 removed outlier: 4.000A pdb=" N GLN H 115 " --> pdb=" O GLN H 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN H 116 " --> pdb=" O GLN H 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 96 Processing helix chain 'C' and resid 96 through 118 Processing helix chain 'J' and resid 6 through 39 removed outlier: 3.820A pdb=" N GLN J 10 " --> pdb=" O LYS J 6 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J 14 " --> pdb=" O GLN J 10 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) Proline residue: J 29 - end of helix Processing helix chain 'J' and resid 48 through 53 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 87 through 93 removed outlier: 4.054A pdb=" N LEU I 93 " --> pdb=" O LYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 108 removed outlier: 7.643A pdb=" N PHE B 147 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN B 167 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 160 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 175 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 14.043A pdb=" N VAL B 186 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 10.063A pdb=" N ASP B 209 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TRP B 188 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER B 214 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 251 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 100 through 110 removed outlier: 6.305A pdb=" N PHE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS I 139 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA I 146 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE I 147 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN I 167 " --> pdb=" O PHE I 147 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG I 173 " --> pdb=" O GLY I 192 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY I 192 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS I 175 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL I 190 " --> pdb=" O LYS I 175 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA I 177 " --> pdb=" O TRP I 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP I 188 " --> pdb=" O ALA I 177 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN I 179 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 14.025A pdb=" N VAL I 186 " --> pdb=" O ASP I 209 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N ASP I 209 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP I 188 " --> pdb=" O ASN I 207 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER I 214 " --> pdb=" O PRO I 208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA I 251 " --> pdb=" O GLY I 232 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY I 100 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU I 358 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE I 360 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR I 104 " --> pdb=" O ILE I 360 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1563 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: 1.44 Time building geometry restraints manager: 1.19 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: 1294 1.32 - 1.44: 2079 1.44 - 1.56: 5751 1.56 - 1.69: 54 1.69 - 1.81: 58 Bond restraints: 9236 Sorted by residual: bond pdb=" CA SER I 183 " pdb=" CB SER I 183 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.74e-02 3.30e+03 7.06e+00 bond pdb=" O13 PC1 I 402 " pdb=" P PC1 I 402 " ideal model delta sigma weight residual 1.652 1.601 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" O13 PC1 H 203 " pdb=" P PC1 H 203 " ideal model delta sigma weight residual 1.652 1.601 0.051 2.00e-02 2.50e+03 6.41e+00 bond pdb=" C11 PC1 A 104 " pdb=" O13 PC1 A 104 " ideal model delta sigma weight residual 1.407 1.457 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C11 PC1 F 102 " pdb=" O13 PC1 F 102 " ideal model delta sigma weight residual 1.407 1.457 -0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 9231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 11497 1.82 - 3.64: 521 3.64 - 5.47: 87 5.47 - 7.29: 15 7.29 - 9.11: 8 Bond angle restraints: 12128 Sorted by residual: angle pdb=" C SER I 183 " pdb=" N LYS I 184 " pdb=" CA LYS I 184 " ideal model delta sigma weight residual 122.72 115.96 6.76 1.38e+00 5.25e-01 2.40e+01 angle pdb=" N GLU B 85 " pdb=" CA GLU B 85 " pdb=" C GLU B 85 " ideal model delta sigma weight residual 112.93 108.24 4.69 1.12e+00 7.97e-01 1.75e+01 angle pdb=" CA GLU G 46 " pdb=" C GLU G 46 " pdb=" N PRO G 47 " ideal model delta sigma weight residual 118.87 122.18 -3.31 9.00e-01 1.23e+00 1.35e+01 angle pdb=" CA CYS B 86 " pdb=" C CYS B 86 " pdb=" O CYS B 86 " ideal model delta sigma weight residual 121.07 117.56 3.51 1.10e+00 8.26e-01 1.02e+01 angle pdb=" CA THR I 180 " pdb=" C THR I 180 " pdb=" O THR I 180 " ideal model delta sigma weight residual 120.70 117.37 3.33 1.08e+00 8.57e-01 9.53e+00 ... (remaining 12123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5008 17.99 - 35.97: 641 35.97 - 53.96: 214 53.96 - 71.94: 68 71.94 - 89.93: 20 Dihedral angle restraints: 5951 sinusoidal: 3250 harmonic: 2701 Sorted by residual: dihedral pdb=" CA THR B 180 " pdb=" C THR B 180 " pdb=" N GLN B 181 " pdb=" CA GLN B 181 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU B 256 " pdb=" C LEU B 256 " pdb=" N ASN B 257 " pdb=" CA ASN B 257 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLN J 13 " pdb=" C GLN J 13 " pdb=" N GLN J 14 " pdb=" CA GLN J 14 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 5948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 763 0.035 - 0.069: 293 0.069 - 0.104: 83 0.104 - 0.139: 37 0.139 - 0.174: 6 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA ASN I 258 " pdb=" N ASN I 258 " pdb=" C ASN I 258 " pdb=" CB ASN I 258 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA GLN I 179 " pdb=" N GLN I 179 " pdb=" C GLN I 179 " pdb=" CB GLN I 179 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C2 PC1 B 408 " pdb=" C1 PC1 B 408 " pdb=" C3 PC1 B 408 " pdb=" O21 PC1 B 408 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1179 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 180 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C THR I 180 " -0.032 2.00e-02 2.50e+03 pdb=" O THR I 180 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN I 181 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 41 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D 42 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 85 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C GLU B 85 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU B 85 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS B 86 " 0.009 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1032 2.74 - 3.28: 7920 3.28 - 3.82: 13203 3.82 - 4.36: 16799 4.36 - 4.90: 29894 Nonbonded interactions: 68848 Sorted by model distance: nonbonded pdb=" O LEU J 12 " pdb=" N LEU J 15 " model vdw 2.196 3.120 nonbonded pdb=" O SER G 5 " pdb=" N ALA G 8 " model vdw 2.197 3.120 nonbonded pdb=" OH TYR E 34 " pdb=" O GLY B 232 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR D 34 " pdb=" O GLY I 232 " model vdw 2.218 3.040 nonbonded pdb=" NZ LYS I 91 " pdb=" OE2 GLU I 287 " model vdw 2.255 3.120 ... (remaining 68843 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' and resid 25 through 103) selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 76 through 402 or resid 405 through 407)) selection = (chain 'I' and (resid 76 through 402 or resid 405 through 407)) } ncs_group { reference = (chain 'C' and resid 63 through 202) selection = (chain 'H' and resid 63 through 202) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'J' } 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: 2.380 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.080 Find NCS groups from input model: 0.160 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:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.011 0.051 9236 Z= 0.536 Angle : 0.907 9.108 12128 Z= 0.418 Chirality : 0.044 0.174 1182 Planarity : 0.003 0.042 1371 Dihedral : 18.201 89.928 4217 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.50 % Allowed : 0.37 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 1.47 (0.28), residues: 931 helix: 2.37 (0.29), residues: 312 sheet: 0.70 (0.26), residues: 398 loop : -0.48 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.008 0.001 TYR D 34 PHE 0.012 0.001 PHE G 27 TRP 0.012 0.001 TRP I 188 HIS 0.008 0.001 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.01124 ( 9236) covalent geometry : angle 0.90688 (12128) hydrogen bonds : bond 0.18172 ( 548) hydrogen bonds : angle 7.16633 ( 1563) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LYS cc_start: 0.9251 (tptp) cc_final: 0.8764 (tppp) REVERT: D 22 GLU cc_start: 0.8278 (pp20) cc_final: 0.7708 (pp20) REVERT: G 9 LYS cc_start: 0.8581 (pttm) cc_final: 0.8375 (pttm) REVERT: G 41 ASP cc_start: 0.8818 (m-30) cc_final: 0.8541 (m-30) REVERT: E 19 LYS cc_start: 0.8235 (mppt) cc_final: 0.7555 (mptt) REVERT: E 22 GLU cc_start: 0.8341 (pp20) cc_final: 0.8081 (pp20) REVERT: H 67 PHE cc_start: 0.8848 (t80) cc_final: 0.8535 (t80) REVERT: H 104 GLU cc_start: 0.8772 (tp30) cc_final: 0.8541 (mm-30) REVERT: H 111 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8686 (tm-30) REVERT: C 75 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8567 (tm-30) REVERT: C 104 GLU cc_start: 0.8772 (tp30) cc_final: 0.8552 (mm-30) REVERT: J 15 LEU cc_start: 0.9222 (tp) cc_final: 0.8984 (tt) REVERT: B 76 CYS cc_start: 0.8486 (m) cc_final: 0.7972 (t) REVERT: B 294 MET cc_start: 0.8754 (mpp) cc_final: 0.8309 (mpp) REVERT: B 296 ASP cc_start: 0.7970 (m-30) cc_final: 0.7672 (m-30) REVERT: I 294 MET cc_start: 0.8740 (mpp) cc_final: 0.8509 (mpp) outliers start: 4 outliers final: 1 residues processed: 212 average time/residue: 0.7285 time to fit residues: 162.5152 Evaluate side-chains 182 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.099031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067198 restraints weight = 16554.199| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.52 r_work: 0.2762 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9236 Z= 0.142 Angle : 0.654 7.999 12128 Z= 0.326 Chirality : 0.042 0.180 1182 Planarity : 0.005 0.049 1371 Dihedral : 19.803 89.039 2441 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.61 % Allowed : 13.93 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.42 (0.29), residues: 931 helix: 3.33 (0.28), residues: 316 sheet: 1.22 (0.26), residues: 388 loop : -0.25 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 29 TYR 0.011 0.001 TYR A 32 PHE 0.021 0.001 PHE C 67 TRP 0.019 0.001 TRP A 27 HIS 0.003 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9236) covalent geometry : angle 0.65436 (12128) hydrogen bonds : bond 0.04158 ( 548) hydrogen bonds : angle 4.58169 ( 1563) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8980 (t0) cc_final: 0.8585 (t0) REVERT: D 16 MET cc_start: 0.9238 (tpp) cc_final: 0.9027 (tpt) REVERT: D 18 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8692 (ttp80) REVERT: D 19 LYS cc_start: 0.9207 (tptp) cc_final: 0.8604 (tppp) REVERT: D 20 MET cc_start: 0.8424 (mtp) cc_final: 0.8106 (mtm) REVERT: D 22 GLU cc_start: 0.8719 (pp20) cc_final: 0.8307 (pp20) REVERT: D 23 ASP cc_start: 0.8865 (m-30) cc_final: 0.8570 (m-30) REVERT: F 37 ASP cc_start: 0.9232 (t70) cc_final: 0.9023 (t0) REVERT: F 38 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8167 (tpp80) REVERT: G 15 LEU cc_start: 0.9080 (tt) cc_final: 0.8717 (tm) REVERT: G 19 SER cc_start: 0.8971 (p) cc_final: 0.8760 (p) REVERT: G 44 MET cc_start: 0.8433 (mpp) cc_final: 0.8179 (mpp) REVERT: E 19 LYS cc_start: 0.8511 (mppt) cc_final: 0.8139 (mptt) REVERT: E 22 GLU cc_start: 0.8633 (pp20) cc_final: 0.8393 (pp20) REVERT: H 67 PHE cc_start: 0.8731 (t80) cc_final: 0.8431 (t80) REVERT: H 72 PHE cc_start: 0.8886 (t80) cc_final: 0.8350 (t80) REVERT: H 75 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8143 (tm-30) REVERT: H 76 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8279 (mptm) REVERT: H 107 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8234 (tm-30) REVERT: H 111 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 75 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8156 (tm-30) REVERT: C 76 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8234 (mptm) REVERT: C 102 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: C 107 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8098 (tm-30) REVERT: C 110 GLN cc_start: 0.8534 (pp30) cc_final: 0.8314 (pp30) REVERT: C 115 GLN cc_start: 0.9477 (tm-30) cc_final: 0.9271 (pp30) REVERT: J 9 LYS cc_start: 0.8875 (mptt) cc_final: 0.8611 (mptt) REVERT: J 14 GLN cc_start: 0.8722 (mt0) cc_final: 0.8306 (tt0) REVERT: J 46 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8526 (mm-30) REVERT: B 76 CYS cc_start: 0.9019 (m) cc_final: 0.8253 (t) REVERT: B 163 GLN cc_start: 0.8727 (mt0) cc_final: 0.8331 (mt0) REVERT: B 294 MET cc_start: 0.9076 (mpp) cc_final: 0.8833 (mpt) REVERT: B 296 ASP cc_start: 0.8075 (m-30) cc_final: 0.7796 (m-30) REVERT: I 84 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8328 (tm-30) REVERT: I 163 GLN cc_start: 0.8630 (mt0) cc_final: 0.8337 (mt0) REVERT: I 294 MET cc_start: 0.9193 (mpp) cc_final: 0.8740 (mpp) outliers start: 21 outliers final: 3 residues processed: 219 average time/residue: 0.6348 time to fit residues: 146.7933 Evaluate side-chains 205 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain B residue 86 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.099344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067673 restraints weight = 16571.424| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.51 r_work: 0.2785 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9236 Z= 0.129 Angle : 0.613 9.833 12128 Z= 0.301 Chirality : 0.041 0.186 1182 Planarity : 0.004 0.043 1371 Dihedral : 19.022 89.679 2441 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.23 % Allowed : 15.67 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.51 (0.29), residues: 931 helix: 3.26 (0.29), residues: 316 sheet: 1.40 (0.26), residues: 388 loop : -0.26 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 18 TYR 0.007 0.001 TYR C 78 PHE 0.013 0.001 PHE B 356 TRP 0.017 0.001 TRP A 27 HIS 0.003 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9236) covalent geometry : angle 0.61310 (12128) hydrogen bonds : bond 0.03499 ( 548) hydrogen bonds : angle 4.17409 ( 1563) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9040 (t0) cc_final: 0.8528 (t0) REVERT: D 16 MET cc_start: 0.9300 (tpp) cc_final: 0.9072 (tpp) REVERT: D 18 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8583 (ttp80) REVERT: D 19 LYS cc_start: 0.9231 (tptp) cc_final: 0.8563 (tppp) REVERT: D 22 GLU cc_start: 0.8729 (pp20) cc_final: 0.8256 (pp20) REVERT: D 23 ASP cc_start: 0.8938 (m-30) cc_final: 0.8645 (m-30) REVERT: F 38 ARG cc_start: 0.8488 (ttm170) cc_final: 0.8249 (tpp80) REVERT: F 40 ASP cc_start: 0.8391 (t0) cc_final: 0.8125 (t0) REVERT: G 44 MET cc_start: 0.8507 (mpp) cc_final: 0.8222 (mpp) REVERT: E 19 LYS cc_start: 0.8538 (mppt) cc_final: 0.7885 (mptp) REVERT: E 29 ARG cc_start: 0.8905 (ttp-110) cc_final: 0.8686 (ttp80) REVERT: H 67 PHE cc_start: 0.8725 (t80) cc_final: 0.8414 (t80) REVERT: H 75 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8226 (tm-30) REVERT: H 104 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8363 (tp30) REVERT: H 107 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8175 (tm-30) REVERT: H 111 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8482 (tm-30) REVERT: H 115 GLN cc_start: 0.8689 (mp10) cc_final: 0.8455 (mp10) REVERT: C 75 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8157 (tm-30) REVERT: C 76 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8239 (mptm) REVERT: C 102 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: C 104 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8382 (tp30) REVERT: C 107 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8049 (tm-30) REVERT: J 14 GLN cc_start: 0.8754 (mt0) cc_final: 0.8466 (tt0) REVERT: J 44 MET cc_start: 0.8350 (mpp) cc_final: 0.8073 (mpp) REVERT: J 46 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8613 (mm-30) REVERT: B 76 CYS cc_start: 0.8993 (m) cc_final: 0.8277 (t) REVERT: B 96 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9106 (pp) REVERT: B 163 GLN cc_start: 0.8637 (mt0) cc_final: 0.8317 (mt0) REVERT: B 195 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8617 (mtm-85) REVERT: B 294 MET cc_start: 0.9191 (mpp) cc_final: 0.8889 (mmm) REVERT: B 296 ASP cc_start: 0.8146 (m-30) cc_final: 0.7860 (m-30) REVERT: I 96 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9104 (pp) REVERT: I 293 ARG cc_start: 0.9288 (mtp-110) cc_final: 0.9009 (ttm110) outliers start: 26 outliers final: 7 residues processed: 214 average time/residue: 0.6601 time to fit residues: 149.2346 Evaluate side-chains 212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066970 restraints weight = 16784.983| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.53 r_work: 0.2768 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9236 Z= 0.151 Angle : 0.617 8.875 12128 Z= 0.303 Chirality : 0.041 0.191 1182 Planarity : 0.004 0.042 1371 Dihedral : 18.705 85.063 2439 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.48 % Allowed : 16.92 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.55 (0.28), residues: 931 helix: 3.20 (0.28), residues: 317 sheet: 1.52 (0.26), residues: 388 loop : -0.29 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 18 TYR 0.007 0.001 TYR H 78 PHE 0.022 0.001 PHE C 67 TRP 0.012 0.001 TRP A 27 HIS 0.004 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9236) covalent geometry : angle 0.61731 (12128) hydrogen bonds : bond 0.03392 ( 548) hydrogen bonds : angle 4.05799 ( 1563) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9098 (t0) cc_final: 0.8612 (t0) REVERT: D 18 ARG cc_start: 0.8903 (ttp80) cc_final: 0.8590 (ttp80) REVERT: D 19 LYS cc_start: 0.9239 (tptp) cc_final: 0.8484 (tppp) REVERT: D 22 GLU cc_start: 0.8698 (pp20) cc_final: 0.8186 (pp20) REVERT: D 38 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8807 (mp) REVERT: F 38 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8279 (tpp80) REVERT: G 13 GLN cc_start: 0.8445 (mt0) cc_final: 0.8158 (mt0) REVERT: G 44 MET cc_start: 0.8550 (mpp) cc_final: 0.8212 (mpp) REVERT: E 18 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8502 (ttp80) REVERT: E 19 LYS cc_start: 0.8357 (mppt) cc_final: 0.7957 (tppp) REVERT: E 22 GLU cc_start: 0.8342 (pp20) cc_final: 0.7690 (pp20) REVERT: E 38 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8882 (mp) REVERT: H 67 PHE cc_start: 0.8738 (t80) cc_final: 0.8429 (t80) REVERT: H 75 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8157 (tm-30) REVERT: H 104 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8405 (tp30) REVERT: H 107 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8155 (tm-30) REVERT: H 111 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8496 (tm-30) REVERT: H 112 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8769 (tm-30) REVERT: C 75 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8183 (tm-30) REVERT: C 102 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: C 104 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8376 (tp30) REVERT: C 107 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 110 GLN cc_start: 0.8317 (pp30) cc_final: 0.8110 (pp30) REVERT: J 14 GLN cc_start: 0.8842 (mt0) cc_final: 0.8565 (tt0) REVERT: J 44 MET cc_start: 0.8390 (mpp) cc_final: 0.8182 (mpp) REVERT: J 46 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8646 (mm-30) REVERT: B 76 CYS cc_start: 0.9026 (m) cc_final: 0.8314 (t) REVERT: B 96 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9114 (pp) REVERT: B 163 GLN cc_start: 0.8670 (mt0) cc_final: 0.8386 (mt0) REVERT: B 195 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8628 (mtm-85) REVERT: B 293 ARG cc_start: 0.9263 (ttm-80) cc_final: 0.8797 (ppp80) REVERT: B 296 ASP cc_start: 0.8199 (m-30) cc_final: 0.7870 (m-30) REVERT: I 96 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9102 (pp) REVERT: I 163 GLN cc_start: 0.8597 (mt0) cc_final: 0.8190 (tt0) REVERT: I 293 ARG cc_start: 0.9305 (mtp-110) cc_final: 0.9053 (mtp-110) REVERT: I 294 MET cc_start: 0.9367 (mmm) cc_final: 0.8981 (mpm) outliers start: 28 outliers final: 8 residues processed: 210 average time/residue: 0.6256 time to fit residues: 139.0259 Evaluate side-chains 206 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.098184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066337 restraints weight = 16712.666| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.50 r_work: 0.2750 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9236 Z= 0.195 Angle : 0.641 10.255 12128 Z= 0.314 Chirality : 0.041 0.193 1182 Planarity : 0.004 0.041 1371 Dihedral : 18.655 84.641 2439 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.99 % Allowed : 18.41 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.50 (0.28), residues: 931 helix: 3.15 (0.29), residues: 317 sheet: 1.51 (0.26), residues: 388 loop : -0.36 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 240 TYR 0.009 0.001 TYR D 34 PHE 0.014 0.001 PHE B 356 TRP 0.012 0.001 TRP A 27 HIS 0.005 0.001 HIS I 271 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9236) covalent geometry : angle 0.64092 (12128) hydrogen bonds : bond 0.03501 ( 548) hydrogen bonds : angle 4.05802 ( 1563) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9075 (t0) cc_final: 0.8625 (t0) REVERT: D 15 GLU cc_start: 0.8988 (pm20) cc_final: 0.8550 (pm20) REVERT: D 19 LYS cc_start: 0.9222 (tptp) cc_final: 0.8807 (tppp) REVERT: D 20 MET cc_start: 0.8410 (mtp) cc_final: 0.8171 (mtm) REVERT: D 22 GLU cc_start: 0.8720 (pp20) cc_final: 0.8307 (pp20) REVERT: D 38 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8814 (mp) REVERT: F 38 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8107 (tpp80) REVERT: F 40 ASP cc_start: 0.8567 (t0) cc_final: 0.8073 (t0) REVERT: G 13 GLN cc_start: 0.8379 (mt0) cc_final: 0.8077 (mt0) REVERT: G 44 MET cc_start: 0.8603 (mpp) cc_final: 0.8248 (mpp) REVERT: E 19 LYS cc_start: 0.8522 (mppt) cc_final: 0.8190 (tppp) REVERT: E 22 GLU cc_start: 0.8501 (pp20) cc_final: 0.7919 (pp20) REVERT: E 38 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8913 (mp) REVERT: H 67 PHE cc_start: 0.8741 (t80) cc_final: 0.8427 (t80) REVERT: H 75 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8172 (tm-30) REVERT: H 104 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8419 (tp30) REVERT: H 107 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8142 (tm-30) REVERT: H 111 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8545 (tm-30) REVERT: H 112 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8788 (pp30) REVERT: C 75 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 102 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: C 104 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8425 (tp30) REVERT: C 107 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8008 (tm-30) REVERT: J 9 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8524 (mptt) REVERT: J 44 MET cc_start: 0.8486 (mpp) cc_final: 0.8259 (mpp) REVERT: J 46 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8628 (mm-30) REVERT: B 76 CYS cc_start: 0.9036 (m) cc_final: 0.8329 (t) REVERT: B 163 GLN cc_start: 0.8702 (mt0) cc_final: 0.8397 (mt0) REVERT: B 195 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8616 (mtm-85) REVERT: B 293 ARG cc_start: 0.9276 (ttm-80) cc_final: 0.9049 (mtp-110) REVERT: B 294 MET cc_start: 0.9157 (mpp) cc_final: 0.8803 (mmt) REVERT: B 296 ASP cc_start: 0.8175 (m-30) cc_final: 0.7880 (m-30) REVERT: I 96 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9105 (pp) REVERT: I 163 GLN cc_start: 0.8627 (mt0) cc_final: 0.8181 (tt0) REVERT: I 293 ARG cc_start: 0.9307 (mtp-110) cc_final: 0.9014 (mtp-110) REVERT: I 294 MET cc_start: 0.9349 (mmm) cc_final: 0.8930 (mpm) outliers start: 24 outliers final: 5 residues processed: 204 average time/residue: 0.6691 time to fit residues: 144.3593 Evaluate side-chains 204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 9 LYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067092 restraints weight = 16548.060| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.55 r_work: 0.2767 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9236 Z= 0.141 Angle : 0.635 9.917 12128 Z= 0.310 Chirality : 0.041 0.193 1182 Planarity : 0.004 0.057 1371 Dihedral : 18.322 86.781 2439 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.36 % Allowed : 21.27 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.65 (0.28), residues: 931 helix: 3.17 (0.29), residues: 317 sheet: 1.64 (0.25), residues: 398 loop : -0.30 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 240 TYR 0.007 0.001 TYR H 78 PHE 0.022 0.001 PHE C 67 TRP 0.011 0.001 TRP I 259 HIS 0.003 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9236) covalent geometry : angle 0.63525 (12128) hydrogen bonds : bond 0.03260 ( 548) hydrogen bonds : angle 3.95326 ( 1563) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9085 (t0) cc_final: 0.8688 (t0) REVERT: D 16 MET cc_start: 0.8406 (mpt) cc_final: 0.8159 (mpt) REVERT: D 19 LYS cc_start: 0.9157 (tptp) cc_final: 0.8769 (tppp) REVERT: D 20 MET cc_start: 0.8399 (mtp) cc_final: 0.8156 (mtm) REVERT: D 22 GLU cc_start: 0.8679 (pp20) cc_final: 0.8314 (pp20) REVERT: D 23 ASP cc_start: 0.8917 (m-30) cc_final: 0.8638 (m-30) REVERT: D 38 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8770 (mp) REVERT: F 38 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8036 (tpp80) REVERT: F 40 ASP cc_start: 0.8488 (t0) cc_final: 0.7994 (t0) REVERT: G 13 GLN cc_start: 0.8440 (mt0) cc_final: 0.8154 (mt0) REVERT: G 44 MET cc_start: 0.8616 (mpp) cc_final: 0.8261 (mpp) REVERT: E 19 LYS cc_start: 0.8549 (mppt) cc_final: 0.8119 (tppp) REVERT: E 22 GLU cc_start: 0.8525 (pp20) cc_final: 0.7945 (pp20) REVERT: E 38 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8849 (mp) REVERT: H 67 PHE cc_start: 0.8743 (t80) cc_final: 0.8434 (t80) REVERT: H 75 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8156 (tm-30) REVERT: H 104 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8404 (tp30) REVERT: H 107 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8071 (tm-30) REVERT: H 111 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8592 (tm-30) REVERT: H 112 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8695 (pp30) REVERT: C 75 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 102 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: C 104 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8412 (tp30) REVERT: C 107 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8059 (tm-30) REVERT: C 115 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9205 (pp30) REVERT: J 9 LYS cc_start: 0.8731 (mptt) cc_final: 0.8326 (mptt) REVERT: J 13 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: J 44 MET cc_start: 0.8524 (mpp) cc_final: 0.8310 (mpp) REVERT: J 46 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8683 (mm-30) REVERT: B 76 CYS cc_start: 0.9008 (m) cc_final: 0.8289 (t) REVERT: B 163 GLN cc_start: 0.8634 (mt0) cc_final: 0.8396 (mt0) REVERT: B 195 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8605 (mtm-85) REVERT: B 293 ARG cc_start: 0.9285 (ttm-80) cc_final: 0.9069 (mtp-110) REVERT: B 294 MET cc_start: 0.9139 (mpp) cc_final: 0.8801 (mmt) REVERT: B 296 ASP cc_start: 0.8166 (m-30) cc_final: 0.7812 (m-30) REVERT: I 163 GLN cc_start: 0.8560 (mt0) cc_final: 0.8143 (tt0) REVERT: I 293 ARG cc_start: 0.9318 (mtp-110) cc_final: 0.9085 (ttm110) outliers start: 19 outliers final: 9 residues processed: 207 average time/residue: 0.6687 time to fit residues: 146.3049 Evaluate side-chains 210 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 195 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 0.0170 chunk 39 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068402 restraints weight = 16716.431| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.53 r_work: 0.2799 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9236 Z= 0.115 Angle : 0.639 10.288 12128 Z= 0.312 Chirality : 0.040 0.187 1182 Planarity : 0.004 0.044 1371 Dihedral : 17.867 89.201 2439 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.36 % Allowed : 21.64 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.72 (0.29), residues: 931 helix: 3.32 (0.29), residues: 314 sheet: 1.61 (0.26), residues: 388 loop : -0.12 (0.45), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 240 TYR 0.007 0.001 TYR H 78 PHE 0.012 0.001 PHE B 356 TRP 0.012 0.001 TRP I 259 HIS 0.003 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9236) covalent geometry : angle 0.63926 (12128) hydrogen bonds : bond 0.03022 ( 548) hydrogen bonds : angle 3.85199 ( 1563) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9110 (t0) cc_final: 0.8775 (t0) REVERT: A 38 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8176 (mtm180) REVERT: D 16 MET cc_start: 0.8456 (mpt) cc_final: 0.8253 (mpt) REVERT: D 18 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8479 (ttp80) REVERT: D 19 LYS cc_start: 0.9186 (tptp) cc_final: 0.8652 (tppp) REVERT: D 22 GLU cc_start: 0.8710 (pp20) cc_final: 0.8272 (pp20) REVERT: D 23 ASP cc_start: 0.8954 (m-30) cc_final: 0.8666 (m-30) REVERT: F 38 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8111 (tpp80) REVERT: F 40 ASP cc_start: 0.8433 (t0) cc_final: 0.7971 (t0) REVERT: G 13 GLN cc_start: 0.8426 (mt0) cc_final: 0.8102 (mt0) REVERT: G 44 MET cc_start: 0.8637 (mpp) cc_final: 0.8276 (mpp) REVERT: E 19 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8192 (tppp) REVERT: E 22 GLU cc_start: 0.8548 (pp20) cc_final: 0.7963 (pp20) REVERT: E 38 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8911 (mp) REVERT: H 67 PHE cc_start: 0.8759 (t80) cc_final: 0.8446 (t80) REVERT: H 72 PHE cc_start: 0.8826 (t80) cc_final: 0.8546 (t80) REVERT: H 75 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8136 (tm-30) REVERT: H 104 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8376 (tp30) REVERT: H 107 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8098 (tm-30) REVERT: H 111 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8612 (tm-30) REVERT: H 112 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8691 (pp30) REVERT: C 75 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8218 (tm-30) REVERT: C 102 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: C 104 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8233 (tp30) REVERT: C 107 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 115 GLN cc_start: 0.9463 (tm-30) cc_final: 0.9211 (pp30) REVERT: J 9 LYS cc_start: 0.8764 (mptt) cc_final: 0.8455 (mptt) REVERT: J 13 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: J 44 MET cc_start: 0.8580 (mpp) cc_final: 0.8360 (mpp) REVERT: J 46 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8678 (mm-30) REVERT: B 76 CYS cc_start: 0.8997 (m) cc_final: 0.8306 (t) REVERT: B 195 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8605 (mtm-85) REVERT: B 293 ARG cc_start: 0.9265 (ttm-80) cc_final: 0.8847 (ppp80) REVERT: I 96 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9106 (pp) REVERT: I 163 GLN cc_start: 0.8527 (mt0) cc_final: 0.8165 (tt0) REVERT: I 293 ARG cc_start: 0.9313 (mtp-110) cc_final: 0.9086 (ttm110) outliers start: 19 outliers final: 3 residues processed: 215 average time/residue: 0.6491 time to fit residues: 147.7441 Evaluate side-chains 208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 81 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068326 restraints weight = 16564.686| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.55 r_work: 0.2800 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9236 Z= 0.121 Angle : 0.657 10.456 12128 Z= 0.321 Chirality : 0.040 0.189 1182 Planarity : 0.004 0.043 1371 Dihedral : 17.613 88.956 2439 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.61 % Allowed : 22.39 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.76 (0.28), residues: 931 helix: 3.35 (0.29), residues: 314 sheet: 1.65 (0.26), residues: 388 loop : -0.13 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 18 TYR 0.007 0.001 TYR H 78 PHE 0.026 0.001 PHE C 67 TRP 0.011 0.001 TRP I 259 HIS 0.003 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9236) covalent geometry : angle 0.65677 (12128) hydrogen bonds : bond 0.03016 ( 548) hydrogen bonds : angle 3.82951 ( 1563) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9117 (t0) cc_final: 0.8819 (t0) REVERT: A 38 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8147 (mtm180) REVERT: D 19 LYS cc_start: 0.9174 (tptp) cc_final: 0.8642 (tppp) REVERT: D 22 GLU cc_start: 0.8728 (pp20) cc_final: 0.8265 (pp20) REVERT: D 38 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8800 (mp) REVERT: F 33 ARG cc_start: 0.8591 (ptp90) cc_final: 0.8346 (ptt-90) REVERT: F 38 ARG cc_start: 0.8517 (ttm170) cc_final: 0.8148 (tpp80) REVERT: F 40 ASP cc_start: 0.8386 (t0) cc_final: 0.7887 (t0) REVERT: G 13 GLN cc_start: 0.8388 (mt0) cc_final: 0.7965 (mt0) REVERT: G 14 GLN cc_start: 0.8508 (mt0) cc_final: 0.7785 (mm-40) REVERT: G 44 MET cc_start: 0.8651 (mpp) cc_final: 0.8291 (mpp) REVERT: E 19 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8168 (tppp) REVERT: E 22 GLU cc_start: 0.8591 (pp20) cc_final: 0.8155 (pp20) REVERT: H 67 PHE cc_start: 0.8750 (t80) cc_final: 0.8439 (t80) REVERT: H 72 PHE cc_start: 0.8819 (t80) cc_final: 0.8561 (t80) REVERT: H 75 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8124 (tm-30) REVERT: H 104 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8298 (tp30) REVERT: H 107 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8112 (tm-30) REVERT: H 111 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8638 (tm-30) REVERT: H 112 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8687 (pp30) REVERT: C 75 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8202 (tm-30) REVERT: C 102 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: C 104 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8251 (tp30) REVERT: C 107 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8005 (tm-30) REVERT: C 115 GLN cc_start: 0.9435 (tm-30) cc_final: 0.9179 (pp30) REVERT: J 44 MET cc_start: 0.8582 (mpp) cc_final: 0.8343 (mpp) REVERT: J 46 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8679 (mm-30) REVERT: B 76 CYS cc_start: 0.9000 (m) cc_final: 0.8297 (t) REVERT: B 163 GLN cc_start: 0.8551 (mt0) cc_final: 0.8177 (tt0) REVERT: B 195 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8600 (mtm-85) REVERT: B 293 ARG cc_start: 0.9261 (ttm-80) cc_final: 0.8846 (ppp80) REVERT: I 163 GLN cc_start: 0.8515 (mt0) cc_final: 0.8168 (tt0) REVERT: I 293 ARG cc_start: 0.9306 (mtp-110) cc_final: 0.8995 (mtp-110) REVERT: I 294 MET cc_start: 0.9351 (mmm) cc_final: 0.8916 (mpm) outliers start: 21 outliers final: 7 residues processed: 209 average time/residue: 0.6821 time to fit residues: 150.6991 Evaluate side-chains 211 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 195 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 67 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.100449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068601 restraints weight = 16638.037| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.55 r_work: 0.2804 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9236 Z= 0.124 Angle : 0.685 11.083 12128 Z= 0.333 Chirality : 0.040 0.188 1182 Planarity : 0.004 0.048 1371 Dihedral : 17.412 87.530 2439 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.11 % Allowed : 22.26 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.80 (0.28), residues: 931 helix: 3.34 (0.29), residues: 314 sheet: 1.72 (0.26), residues: 386 loop : -0.12 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 18 TYR 0.007 0.001 TYR H 78 PHE 0.012 0.001 PHE I 83 TRP 0.010 0.001 TRP I 259 HIS 0.003 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9236) covalent geometry : angle 0.68465 (12128) hydrogen bonds : bond 0.02973 ( 548) hydrogen bonds : angle 3.81463 ( 1563) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9109 (t0) cc_final: 0.8842 (t0) REVERT: A 38 ARG cc_start: 0.8439 (mtp85) cc_final: 0.8139 (mtm180) REVERT: D 19 LYS cc_start: 0.9174 (tptp) cc_final: 0.8583 (tppp) REVERT: D 22 GLU cc_start: 0.8695 (pp20) cc_final: 0.8279 (pp20) REVERT: D 23 ASP cc_start: 0.8874 (m-30) cc_final: 0.8443 (m-30) REVERT: D 38 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8853 (mp) REVERT: F 33 ARG cc_start: 0.8591 (ptp90) cc_final: 0.8339 (ptt-90) REVERT: F 38 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8186 (tpp80) REVERT: F 40 ASP cc_start: 0.8376 (t0) cc_final: 0.7915 (t0) REVERT: G 13 GLN cc_start: 0.8365 (mt0) cc_final: 0.7991 (mt0) REVERT: G 44 MET cc_start: 0.8675 (mpp) cc_final: 0.8313 (mpp) REVERT: E 19 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8195 (tppp) REVERT: E 22 GLU cc_start: 0.8591 (pp20) cc_final: 0.8158 (pp20) REVERT: H 67 PHE cc_start: 0.8748 (t80) cc_final: 0.8437 (t80) REVERT: H 72 PHE cc_start: 0.8808 (t80) cc_final: 0.8561 (t80) REVERT: H 75 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8121 (tm-30) REVERT: H 104 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8302 (tp30) REVERT: H 107 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8158 (tm-30) REVERT: H 111 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8561 (tm-30) REVERT: H 112 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8671 (pp30) REVERT: C 75 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 102 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: C 104 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8266 (tp30) REVERT: C 107 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8010 (tm-30) REVERT: J 9 LYS cc_start: 0.8654 (mptt) cc_final: 0.8419 (mptt) REVERT: J 44 MET cc_start: 0.8597 (mpp) cc_final: 0.8348 (mpp) REVERT: J 46 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8681 (mm-30) REVERT: B 76 CYS cc_start: 0.8986 (m) cc_final: 0.8297 (t) REVERT: B 163 GLN cc_start: 0.8545 (mt0) cc_final: 0.8188 (tt0) REVERT: B 293 ARG cc_start: 0.9254 (ttm-80) cc_final: 0.8858 (ppp80) REVERT: I 163 GLN cc_start: 0.8512 (mt0) cc_final: 0.8186 (tt0) outliers start: 17 outliers final: 8 residues processed: 207 average time/residue: 0.6872 time to fit residues: 150.4018 Evaluate side-chains 208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 86 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.099542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067706 restraints weight = 16539.243| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.56 r_work: 0.2783 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9236 Z= 0.180 Angle : 0.876 38.259 12128 Z= 0.417 Chirality : 0.041 0.192 1182 Planarity : 0.006 0.103 1371 Dihedral : 17.418 89.399 2439 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.62 % Allowed : 23.51 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.77 (0.28), residues: 931 helix: 3.32 (0.29), residues: 314 sheet: 1.74 (0.26), residues: 386 loop : -0.21 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 18 TYR 0.008 0.001 TYR D 34 PHE 0.028 0.001 PHE C 67 TRP 0.007 0.001 TRP I 188 HIS 0.003 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9236) covalent geometry : angle 0.87552 (12128) hydrogen bonds : bond 0.03166 ( 548) hydrogen bonds : angle 3.87789 ( 1563) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9118 (t0) cc_final: 0.8853 (t0) REVERT: A 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.7985 (mmm-85) REVERT: D 18 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8303 (ttp80) REVERT: D 19 LYS cc_start: 0.9167 (tptp) cc_final: 0.8490 (tppp) REVERT: D 22 GLU cc_start: 0.8704 (pp20) cc_final: 0.8259 (pp20) REVERT: D 23 ASP cc_start: 0.8859 (m-30) cc_final: 0.8395 (m-30) REVERT: D 38 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8905 (mp) REVERT: F 38 ARG cc_start: 0.8526 (ttm170) cc_final: 0.8191 (tpp80) REVERT: F 40 ASP cc_start: 0.8392 (t0) cc_final: 0.7922 (t0) REVERT: G 13 GLN cc_start: 0.8393 (mt0) cc_final: 0.8013 (mt0) REVERT: G 44 MET cc_start: 0.8686 (mpp) cc_final: 0.8347 (mpp) REVERT: E 19 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8196 (tppp) REVERT: E 22 GLU cc_start: 0.8582 (pp20) cc_final: 0.8105 (pp20) REVERT: H 67 PHE cc_start: 0.8754 (t80) cc_final: 0.8443 (t80) REVERT: H 72 PHE cc_start: 0.8845 (t80) cc_final: 0.8586 (t80) REVERT: H 75 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8140 (tm-30) REVERT: H 104 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8246 (tp30) REVERT: H 107 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8164 (tm-30) REVERT: H 111 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8626 (tm-30) REVERT: H 112 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8681 (pp30) REVERT: C 75 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 102 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: C 104 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8249 (tp30) REVERT: C 107 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 112 GLN cc_start: 0.9215 (tt0) cc_final: 0.8946 (tm-30) REVERT: J 9 LYS cc_start: 0.8563 (mptt) cc_final: 0.8273 (mptt) REVERT: J 44 MET cc_start: 0.8592 (mpp) cc_final: 0.8340 (mpp) REVERT: J 46 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8667 (mm-30) REVERT: B 76 CYS cc_start: 0.9000 (m) cc_final: 0.8291 (t) REVERT: B 163 GLN cc_start: 0.8587 (mt0) cc_final: 0.8204 (tt0) REVERT: B 293 ARG cc_start: 0.9243 (ttm-80) cc_final: 0.8860 (ppp80) REVERT: I 163 GLN cc_start: 0.8554 (mt0) cc_final: 0.8202 (tt0) REVERT: I 293 ARG cc_start: 0.9281 (mtp-110) cc_final: 0.8991 (ttm110) REVERT: I 294 MET cc_start: 0.9378 (mmm) cc_final: 0.9126 (mpp) outliers start: 13 outliers final: 7 residues processed: 207 average time/residue: 0.7054 time to fit residues: 154.1288 Evaluate side-chains 208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain B residue 86 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067498 restraints weight = 16539.277| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.53 r_work: 0.2776 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9236 Z= 0.163 Angle : 0.718 11.226 12128 Z= 0.351 Chirality : 0.041 0.192 1182 Planarity : 0.005 0.076 1371 Dihedral : 17.389 88.966 2439 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.49 % Allowed : 24.13 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 2.73 (0.28), residues: 931 helix: 3.22 (0.29), residues: 318 sheet: 1.73 (0.26), residues: 386 loop : -0.22 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 18 TYR 0.008 0.001 TYR D 34 PHE 0.014 0.001 PHE H 101 TRP 0.011 0.001 TRP A 27 HIS 0.004 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9236) covalent geometry : angle 0.71843 (12128) hydrogen bonds : bond 0.03255 ( 548) hydrogen bonds : angle 3.90470 ( 1563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4082.28 seconds wall clock time: 70 minutes 7.21 seconds (4207.21 seconds total)