Starting phenix.real_space_refine on Sun Dec 29 01:08:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vd2_31904/12_2024/7vd2_31904_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vd2_31904/12_2024/7vd2_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_31904/12_2024/7vd2_31904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vd2_31904/12_2024/7vd2_31904.map" model { file = "/net/cci-nas-00/data/ceres_data/7vd2_31904/12_2024/7vd2_31904_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vd2_31904/12_2024/7vd2_31904_neut.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.08, per 1000 atoms: 0.67 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: 3.05 Conformation dependent library (CDL) restraints added in 939.9 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: 0.92 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: 2.60 Time building geometry restraints manager: 3.12 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 67 or resid 101 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 76 through 361 or resid 401 through 402 or resid 405 throu \ gh 407)) selection = (chain 'I' and (resid 76 through 361 or resid 401 through 402 or resid 405 throu \ gh 407)) } ncs_group { reference = (chain 'C' and (resid 63 through 118 or resid 201 through 202)) selection = (chain 'H' and (resid 63 through 118 or resid 201 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.780 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- 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= 0.686 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP I 188 HIS 0.008 0.001 HIS B 271 PHE 0.012 0.001 PHE G 27 TYR 0.008 0.001 TYR D 34 ARG 0.006 0.001 ARG A 33 *********************** 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 : 0.942 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: 1.5084 time to fit residues: 337.7409 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 : 1.016 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1811 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= 0.186 Angle : 0.646 7.707 12128 Z= 0.322 Chirality : 0.042 0.175 1182 Planarity : 0.004 0.047 1371 Dihedral : 19.808 89.565 2441 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.24 % Allowed : 14.18 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.29), residues: 931 helix: 3.35 (0.28), residues: 316 sheet: 1.22 (0.26), residues: 388 loop : -0.22 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 27 HIS 0.002 0.001 HIS I 271 PHE 0.021 0.001 PHE C 67 TYR 0.010 0.001 TYR A 32 ARG 0.008 0.001 ARG D 29 *********************** 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 234 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.011 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: 0.9157 (t0) cc_final: 0.8780 (t0) REVERT: D 18 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8595 (ttp80) REVERT: D 19 LYS cc_start: 0.9270 (tptp) cc_final: 0.8565 (tppp) REVERT: D 20 MET cc_start: 0.8668 (mtp) cc_final: 0.8367 (mtm) REVERT: D 22 GLU cc_start: 0.8449 (pp20) cc_final: 0.8113 (pp20) REVERT: E 19 LYS cc_start: 0.8461 (mppt) cc_final: 0.8087 (mptt) REVERT: H 67 PHE cc_start: 0.8840 (t80) cc_final: 0.8484 (t80) REVERT: H 72 PHE cc_start: 0.9061 (t80) cc_final: 0.8651 (t80) REVERT: H 75 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8345 (tm-30) REVERT: H 76 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8309 (mptm) REVERT: H 104 GLU cc_start: 0.8727 (tp30) cc_final: 0.8508 (mm-30) REVERT: H 107 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8313 (tm-30) REVERT: H 111 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8663 (tm-30) REVERT: H 112 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8685 (tm-30) REVERT: C 75 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8363 (tm-30) REVERT: C 76 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8256 (mptm) REVERT: C 102 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 104 GLU cc_start: 0.8746 (tp30) cc_final: 0.8531 (mm-30) REVERT: C 107 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8137 (tm-30) REVERT: C 110 GLN cc_start: 0.8642 (pp30) cc_final: 0.8421 (pp30) REVERT: J 9 LYS cc_start: 0.8997 (mptt) cc_final: 0.8683 (mptt) REVERT: J 14 GLN cc_start: 0.8874 (mt0) cc_final: 0.8581 (tt0) REVERT: B 76 CYS cc_start: 0.8383 (m) cc_final: 0.7943 (t) REVERT: B 163 GLN cc_start: 0.8420 (mt0) cc_final: 0.8039 (mt0) REVERT: B 294 MET cc_start: 0.8664 (mpp) cc_final: 0.8461 (mpt) REVERT: B 296 ASP cc_start: 0.7953 (m-30) cc_final: 0.7641 (m-30) REVERT: I 163 GLN cc_start: 0.8309 (mt0) cc_final: 0.7966 (mt0) REVERT: I 176 MET cc_start: 0.8161 (mtt) cc_final: 0.7954 (mtm) REVERT: I 240 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7743 (mtm110) outliers start: 18 outliers final: 2 residues processed: 218 average time/residue: 1.3855 time to fit residues: 319.6883 Evaluate side-chains 202 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9236 Z= 0.259 Angle : 0.629 8.071 12128 Z= 0.310 Chirality : 0.042 0.193 1182 Planarity : 0.004 0.044 1371 Dihedral : 19.167 89.147 2441 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.23 % Allowed : 16.42 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 931 helix: 3.18 (0.28), residues: 316 sheet: 1.46 (0.26), residues: 398 loop : -0.31 (0.46), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 27 HIS 0.005 0.001 HIS I 271 PHE 0.014 0.001 PHE B 356 TYR 0.006 0.001 TYR C 78 ARG 0.007 0.001 ARG B 240 *********************** 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 232 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9200 (t0) cc_final: 0.8734 (t0) REVERT: D 15 GLU cc_start: 0.8860 (pm20) cc_final: 0.7967 (pm20) REVERT: D 18 ARG cc_start: 0.8742 (ttp80) cc_final: 0.8296 (ttp80) REVERT: D 19 LYS cc_start: 0.9277 (tptp) cc_final: 0.8435 (tppp) REVERT: D 20 MET cc_start: 0.8670 (mtp) cc_final: 0.8446 (mtm) REVERT: D 22 GLU cc_start: 0.8454 (pp20) cc_final: 0.8044 (pp20) REVERT: G 15 LEU cc_start: 0.9190 (tt) cc_final: 0.8979 (tt) REVERT: E 22 GLU cc_start: 0.8089 (pp20) cc_final: 0.7879 (pp20) REVERT: E 29 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8638 (ttp80) REVERT: H 67 PHE cc_start: 0.8820 (t80) cc_final: 0.8453 (t80) REVERT: H 75 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8297 (tm-30) REVERT: H 104 GLU cc_start: 0.8740 (tp30) cc_final: 0.8514 (mm-30) REVERT: H 107 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8275 (tm-30) REVERT: H 111 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8676 (tm-30) REVERT: H 112 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8639 (tm-30) REVERT: C 75 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 102 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: C 104 GLU cc_start: 0.8749 (tp30) cc_final: 0.8538 (mm-30) REVERT: C 107 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8094 (tm-30) REVERT: J 9 LYS cc_start: 0.8961 (mptt) cc_final: 0.8676 (mptt) REVERT: B 76 CYS cc_start: 0.8369 (m) cc_final: 0.8016 (t) REVERT: B 96 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9195 (pp) REVERT: B 163 GLN cc_start: 0.8413 (mt0) cc_final: 0.7989 (mt0) REVERT: B 195 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8628 (mtm-85) REVERT: B 294 MET cc_start: 0.8786 (mpp) cc_final: 0.8498 (mmm) REVERT: B 296 ASP cc_start: 0.8021 (m-30) cc_final: 0.7682 (m-30) REVERT: I 84 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7800 (tm-30) REVERT: I 88 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7943 (ttm110) REVERT: I 96 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9183 (pp) REVERT: I 163 GLN cc_start: 0.8293 (mt0) cc_final: 0.8046 (mt0) REVERT: I 176 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: I 240 ARG cc_start: 0.8036 (mtm110) cc_final: 0.7804 (mtm110) REVERT: I 294 MET cc_start: 0.9021 (mmm) cc_final: 0.8719 (mpm) outliers start: 26 outliers final: 8 residues processed: 210 average time/residue: 1.3697 time to fit residues: 304.4678 Evaluate side-chains 211 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 76 LYS 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 195 ARG Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 176 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- 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** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2353 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= 0.202 Angle : 0.616 8.219 12128 Z= 0.301 Chirality : 0.041 0.189 1182 Planarity : 0.004 0.041 1371 Dihedral : 18.838 85.164 2439 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.36 % Allowed : 16.92 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.29), residues: 931 helix: 3.18 (0.29), residues: 316 sheet: 1.45 (0.26), residues: 390 loop : -0.27 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 27 HIS 0.003 0.001 HIS I 271 PHE 0.021 0.001 PHE C 67 TYR 0.007 0.001 TYR H 78 ARG 0.013 0.001 ARG B 240 *********************** 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: 27 poor density : 205 time to evaluate : 1.056 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: 0.9222 (t0) cc_final: 0.8751 (t0) REVERT: D 18 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8481 (ttp80) REVERT: D 19 LYS cc_start: 0.9242 (tptp) cc_final: 0.8403 (tppp) REVERT: D 20 MET cc_start: 0.8684 (mtp) cc_final: 0.8384 (mtm) REVERT: D 22 GLU cc_start: 0.8430 (pp20) cc_final: 0.8008 (pp20) REVERT: D 38 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8794 (mp) REVERT: G 15 LEU cc_start: 0.9224 (tt) cc_final: 0.9023 (tt) REVERT: E 19 LYS cc_start: 0.8396 (mppt) cc_final: 0.8047 (mptp) REVERT: E 22 GLU cc_start: 0.8223 (pp20) cc_final: 0.7983 (pp20) REVERT: E 23 ASP cc_start: 0.8846 (m-30) cc_final: 0.8615 (m-30) REVERT: H 67 PHE cc_start: 0.8832 (t80) cc_final: 0.8469 (t80) REVERT: H 75 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8296 (tm-30) REVERT: H 104 GLU cc_start: 0.8721 (tp30) cc_final: 0.8508 (mm-30) REVERT: H 107 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8203 (tm-30) REVERT: H 111 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8637 (tm-30) REVERT: C 75 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 102 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: C 104 GLU cc_start: 0.8716 (tp30) cc_final: 0.8270 (tp30) REVERT: C 107 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8038 (tm-30) REVERT: C 110 GLN cc_start: 0.8435 (pp30) cc_final: 0.8215 (pp30) REVERT: J 9 LYS cc_start: 0.8914 (mptt) cc_final: 0.8607 (mptt) REVERT: J 13 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: B 76 CYS cc_start: 0.8361 (m) cc_final: 0.7977 (t) REVERT: B 96 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9197 (pp) REVERT: B 163 GLN cc_start: 0.8350 (mt0) cc_final: 0.8030 (mt0) REVERT: B 195 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8631 (mtm-85) REVERT: B 294 MET cc_start: 0.8756 (mpp) cc_final: 0.8524 (mpp) REVERT: B 296 ASP cc_start: 0.8035 (m-30) cc_final: 0.7714 (m-30) REVERT: I 293 ARG cc_start: 0.8774 (mtp-110) cc_final: 0.8505 (ttm110) outliers start: 27 outliers final: 11 residues processed: 210 average time/residue: 1.3543 time to fit residues: 301.0219 Evaluate side-chains 210 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 6 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 102 GLU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9236 Z= 0.247 Angle : 0.629 8.923 12128 Z= 0.306 Chirality : 0.041 0.191 1182 Planarity : 0.004 0.041 1371 Dihedral : 18.675 84.986 2439 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.11 % Allowed : 18.78 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.29), residues: 931 helix: 3.18 (0.29), residues: 317 sheet: 1.53 (0.26), residues: 388 loop : -0.29 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 27 HIS 0.004 0.001 HIS I 271 PHE 0.013 0.001 PHE B 356 TYR 0.007 0.001 TYR D 34 ARG 0.009 0.001 ARG B 240 *********************** 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 225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8418 (ptp90) cc_final: 0.8213 (ptp90) REVERT: A 37 ASP cc_start: 0.9245 (t0) cc_final: 0.8809 (t0) REVERT: D 15 GLU cc_start: 0.8794 (pm20) cc_final: 0.8188 (pm20) REVERT: D 19 LYS cc_start: 0.9248 (tptp) cc_final: 0.8809 (tppp) REVERT: D 22 GLU cc_start: 0.8432 (pp20) cc_final: 0.8059 (pp20) REVERT: D 38 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8830 (mp) REVERT: G 9 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8656 (pptt) REVERT: G 13 GLN cc_start: 0.8269 (mt0) cc_final: 0.7819 (mt0) REVERT: E 19 LYS cc_start: 0.8352 (mppt) cc_final: 0.7655 (tppp) REVERT: E 22 GLU cc_start: 0.8254 (pp20) cc_final: 0.7631 (pp20) REVERT: E 23 ASP cc_start: 0.8881 (m-30) cc_final: 0.8346 (m-30) REVERT: H 67 PHE cc_start: 0.8837 (t80) cc_final: 0.8475 (t80) REVERT: H 75 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8314 (tm-30) REVERT: H 104 GLU cc_start: 0.8722 (tp30) cc_final: 0.8131 (tp30) REVERT: H 107 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8177 (tm-30) REVERT: H 111 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8246 (tm-30) REVERT: H 115 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8491 (mm-40) REVERT: C 75 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8422 (tm-30) REVERT: C 102 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: C 104 GLU cc_start: 0.8724 (tp30) cc_final: 0.8283 (tp30) REVERT: C 107 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7980 (tm-30) REVERT: C 115 GLN cc_start: 0.9433 (tm-30) cc_final: 0.9211 (pp30) REVERT: J 9 LYS cc_start: 0.8943 (mptt) cc_final: 0.8635 (mptt) REVERT: J 13 GLN cc_start: 0.8289 (pm20) cc_final: 0.8040 (pm20) REVERT: B 76 CYS cc_start: 0.8353 (m) cc_final: 0.8026 (t) REVERT: B 163 GLN cc_start: 0.8353 (mt0) cc_final: 0.8045 (mt0) REVERT: B 195 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8628 (mtm-85) REVERT: B 294 MET cc_start: 0.8741 (mpp) cc_final: 0.8394 (mmt) REVERT: B 296 ASP cc_start: 0.8043 (m-30) cc_final: 0.7722 (m-30) REVERT: I 88 ARG cc_start: 0.8419 (ttm110) cc_final: 0.8193 (tpp80) REVERT: I 96 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9174 (pp) REVERT: I 163 GLN cc_start: 0.8247 (mt0) cc_final: 0.7913 (tt0) REVERT: I 293 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8516 (mtp-110) REVERT: I 294 MET cc_start: 0.8854 (mpp) cc_final: 0.8506 (mpm) outliers start: 25 outliers final: 11 residues processed: 205 average time/residue: 1.3781 time to fit residues: 299.4174 Evaluate side-chains 207 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 6 LYS Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 114 LEU 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 14 GLN Chi-restraints excluded: chain J residue 50 LEU 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 51 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9236 Z= 0.347 Angle : 0.680 8.722 12128 Z= 0.330 Chirality : 0.043 0.203 1182 Planarity : 0.004 0.056 1371 Dihedral : 18.751 85.496 2439 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.23 % Allowed : 20.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.29), residues: 931 helix: 3.17 (0.29), residues: 317 sheet: 1.59 (0.26), residues: 398 loop : -0.39 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 27 HIS 0.005 0.001 HIS I 271 PHE 0.022 0.001 PHE C 67 TYR 0.010 0.001 TYR E 34 ARG 0.018 0.001 ARG B 240 *********************** 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 220 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9245 (t0) cc_final: 0.8865 (t0) REVERT: D 22 GLU cc_start: 0.8435 (pp20) cc_final: 0.8133 (pp20) REVERT: D 23 ASP cc_start: 0.8829 (m-30) cc_final: 0.8480 (m-30) REVERT: D 38 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8863 (mp) REVERT: G 13 GLN cc_start: 0.8304 (mt0) cc_final: 0.8103 (mt0) REVERT: E 19 LYS cc_start: 0.8548 (mppt) cc_final: 0.7973 (tppp) REVERT: E 22 GLU cc_start: 0.8326 (pp20) cc_final: 0.7765 (pp20) REVERT: E 23 ASP cc_start: 0.8923 (m-30) cc_final: 0.8405 (m-30) REVERT: H 67 PHE cc_start: 0.8836 (t80) cc_final: 0.8468 (t80) REVERT: H 75 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8286 (tm-30) REVERT: H 104 GLU cc_start: 0.8721 (tp30) cc_final: 0.8133 (tp30) REVERT: H 107 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8119 (tm-30) REVERT: H 111 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8246 (tm-30) REVERT: H 115 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8637 (mm-40) REVERT: C 75 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 102 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: C 104 GLU cc_start: 0.8727 (tp30) cc_final: 0.8103 (tp30) REVERT: C 107 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8078 (tm-30) REVERT: C 115 GLN cc_start: 0.9362 (tm-30) cc_final: 0.9132 (pp30) REVERT: J 9 LYS cc_start: 0.9020 (mptt) cc_final: 0.8784 (mptt) REVERT: B 76 CYS cc_start: 0.8414 (m) cc_final: 0.8019 (t) REVERT: B 96 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9201 (pp) REVERT: B 163 GLN cc_start: 0.8424 (mt0) cc_final: 0.8018 (mt0) REVERT: B 195 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8575 (mtm-85) REVERT: I 96 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9180 (pp) REVERT: I 163 GLN cc_start: 0.8358 (mt0) cc_final: 0.7968 (tt0) outliers start: 26 outliers final: 10 residues processed: 199 average time/residue: 1.3839 time to fit residues: 292.4050 Evaluate side-chains 205 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 6 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 H residue 114 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9236 Z= 0.188 Angle : 0.653 9.076 12128 Z= 0.316 Chirality : 0.041 0.189 1182 Planarity : 0.004 0.059 1371 Dihedral : 18.241 87.496 2439 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.49 % Allowed : 21.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.29), residues: 931 helix: 3.21 (0.29), residues: 317 sheet: 1.59 (0.26), residues: 388 loop : -0.20 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 259 HIS 0.003 0.001 HIS B 220 PHE 0.013 0.001 PHE B 356 TYR 0.007 0.001 TYR H 78 ARG 0.018 0.001 ARG B 240 *********************** 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 223 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.283 Fit side-chains REVERT: A 37 ASP cc_start: 0.9231 (t0) cc_final: 0.8908 (t0) REVERT: D 18 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8350 (ttp80) REVERT: D 19 LYS cc_start: 0.9162 (tptp) cc_final: 0.8564 (tppp) REVERT: D 22 GLU cc_start: 0.8401 (pp20) cc_final: 0.8062 (pp20) REVERT: D 23 ASP cc_start: 0.8814 (m-30) cc_final: 0.8455 (m-30) REVERT: D 38 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8805 (mp) REVERT: G 9 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8630 (pmtt) REVERT: E 19 LYS cc_start: 0.8496 (mppt) cc_final: 0.7969 (tppp) REVERT: E 22 GLU cc_start: 0.8312 (pp20) cc_final: 0.7726 (pp20) REVERT: E 23 ASP cc_start: 0.8942 (m-30) cc_final: 0.8446 (m-30) REVERT: H 67 PHE cc_start: 0.8838 (t80) cc_final: 0.8481 (t80) REVERT: H 75 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8273 (tm-30) REVERT: H 104 GLU cc_start: 0.8690 (tp30) cc_final: 0.8118 (tp30) REVERT: H 107 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8045 (tm-30) REVERT: H 111 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8254 (tm-30) REVERT: H 112 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8629 (pp30) REVERT: H 115 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8611 (mm110) REVERT: C 75 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 102 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: C 104 GLU cc_start: 0.8710 (tp30) cc_final: 0.8093 (tp30) REVERT: C 107 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 115 GLN cc_start: 0.9355 (tm-30) cc_final: 0.9140 (pp30) REVERT: J 9 LYS cc_start: 0.8995 (mptt) cc_final: 0.8647 (mptt) REVERT: J 13 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: B 76 CYS cc_start: 0.8340 (m) cc_final: 0.7954 (t) REVERT: B 163 GLN cc_start: 0.8318 (mt0) cc_final: 0.8047 (mt0) REVERT: B 195 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8572 (mtm-85) REVERT: B 293 ARG cc_start: 0.8623 (ttm110) cc_final: 0.8214 (mtp-110) REVERT: B 294 MET cc_start: 0.8835 (mmm) cc_final: 0.8552 (mpm) REVERT: B 296 ASP cc_start: 0.7865 (m-30) cc_final: 0.7547 (m-30) REVERT: I 163 GLN cc_start: 0.8221 (mt0) cc_final: 0.7923 (tt0) outliers start: 20 outliers final: 9 residues processed: 208 average time/residue: 1.3957 time to fit residues: 308.5847 Evaluate side-chains 208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 12 LEU 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 J residue 13 GLN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 78 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 0.041 9236 Z= 0.169 Angle : 0.682 9.342 12128 Z= 0.330 Chirality : 0.041 0.187 1182 Planarity : 0.004 0.069 1371 Dihedral : 17.868 89.643 2439 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.11 % Allowed : 22.76 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.29), residues: 931 helix: 3.24 (0.29), residues: 317 sheet: 1.65 (0.26), residues: 388 loop : -0.18 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 259 HIS 0.002 0.001 HIS I 220 PHE 0.026 0.001 PHE C 67 TYR 0.007 0.001 TYR H 78 ARG 0.018 0.001 ARG B 240 *********************** 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 223 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9225 (t0) cc_final: 0.9002 (t0) REVERT: D 18 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8447 (ttp80) REVERT: D 19 LYS cc_start: 0.9142 (tptp) cc_final: 0.8513 (tppp) REVERT: D 22 GLU cc_start: 0.8361 (pp20) cc_final: 0.8007 (pp20) REVERT: D 38 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8768 (mp) REVERT: E 19 LYS cc_start: 0.8510 (mppt) cc_final: 0.7803 (tppp) REVERT: E 22 GLU cc_start: 0.8283 (pp20) cc_final: 0.7753 (pp20) REVERT: E 23 ASP cc_start: 0.8943 (m-30) cc_final: 0.8271 (m-30) REVERT: H 67 PHE cc_start: 0.8838 (t80) cc_final: 0.8481 (t80) REVERT: H 75 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8242 (tm-30) REVERT: H 104 GLU cc_start: 0.8688 (tp30) cc_final: 0.8106 (tp30) REVERT: H 105 LYS cc_start: 0.8979 (tttm) cc_final: 0.8771 (tttp) REVERT: H 107 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8092 (tm-30) REVERT: H 111 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8551 (tm-30) REVERT: H 112 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8603 (pp30) REVERT: C 75 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 102 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: C 104 GLU cc_start: 0.8710 (tp30) cc_final: 0.8105 (tp30) REVERT: C 107 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 115 GLN cc_start: 0.9330 (tm-30) cc_final: 0.9087 (pp30) REVERT: B 76 CYS cc_start: 0.8339 (m) cc_final: 0.7971 (t) REVERT: B 195 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8617 (mtm-85) REVERT: B 293 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8213 (mtp-110) REVERT: B 294 MET cc_start: 0.8831 (mmm) cc_final: 0.8620 (mpm) REVERT: I 84 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7983 (tm-30) REVERT: I 163 GLN cc_start: 0.8177 (mt0) cc_final: 0.7952 (tt0) REVERT: I 293 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.8480 (ttm110) outliers start: 17 outliers final: 7 residues processed: 213 average time/residue: 1.3117 time to fit residues: 296.5689 Evaluate side-chains 207 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 28 ILE 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 50 LEU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9236 Z= 0.190 Angle : 0.705 10.028 12128 Z= 0.344 Chirality : 0.041 0.188 1182 Planarity : 0.005 0.073 1371 Dihedral : 17.667 88.585 2439 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.87 % Allowed : 23.63 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.29), residues: 931 helix: 3.26 (0.29), residues: 317 sheet: 1.67 (0.26), residues: 388 loop : -0.14 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 259 HIS 0.003 0.001 HIS B 220 PHE 0.025 0.001 PHE H 72 TYR 0.007 0.001 TYR H 78 ARG 0.019 0.001 ARG I 240 *********************** 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 220 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.9226 (t0) cc_final: 0.9020 (t0) REVERT: D 18 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8396 (ttp80) REVERT: D 19 LYS cc_start: 0.9102 (tptp) cc_final: 0.8221 (tppp) REVERT: D 22 GLU cc_start: 0.8351 (pp20) cc_final: 0.7951 (pp20) REVERT: D 23 ASP cc_start: 0.8741 (m-30) cc_final: 0.8066 (m-30) REVERT: D 38 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8802 (mp) REVERT: F 40 ASP cc_start: 0.8456 (t0) cc_final: 0.8031 (t0) REVERT: E 19 LYS cc_start: 0.8546 (mppt) cc_final: 0.7987 (tppp) REVERT: E 22 GLU cc_start: 0.8299 (pp20) cc_final: 0.7842 (pp20) REVERT: E 23 ASP cc_start: 0.8940 (m-30) cc_final: 0.8246 (m-30) REVERT: H 67 PHE cc_start: 0.8826 (t80) cc_final: 0.8468 (t80) REVERT: H 75 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8231 (tm-30) REVERT: H 104 GLU cc_start: 0.8683 (tp30) cc_final: 0.8066 (tp30) REVERT: H 105 LYS cc_start: 0.8982 (tttm) cc_final: 0.8777 (tttp) REVERT: H 107 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8099 (tm-30) REVERT: H 111 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8578 (tm-30) REVERT: H 112 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8577 (pp30) REVERT: C 75 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 102 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: C 104 GLU cc_start: 0.8707 (tp30) cc_final: 0.8097 (tp30) REVERT: C 107 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8018 (tm-30) REVERT: J 9 LYS cc_start: 0.8862 (mptt) cc_final: 0.8564 (mptt) REVERT: J 46 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8191 (mm-30) REVERT: B 76 CYS cc_start: 0.8334 (m) cc_final: 0.7988 (t) REVERT: B 163 GLN cc_start: 0.8232 (mt0) cc_final: 0.7951 (tt0) REVERT: B 195 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8622 (mtm-85) REVERT: B 294 MET cc_start: 0.8818 (mmm) cc_final: 0.8485 (mmt) outliers start: 15 outliers final: 7 residues processed: 210 average time/residue: 1.3900 time to fit residues: 309.0941 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 : 1.000 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain I residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9236 Z= 0.220 Angle : 0.734 11.170 12128 Z= 0.357 Chirality : 0.041 0.190 1182 Planarity : 0.005 0.080 1371 Dihedral : 17.562 89.608 2439 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.99 % Allowed : 24.13 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.28), residues: 931 helix: 3.53 (0.29), residues: 300 sheet: 1.69 (0.26), residues: 388 loop : -0.04 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 259 HIS 0.003 0.001 HIS B 220 PHE 0.027 0.001 PHE C 67 TYR 0.008 0.001 TYR D 34 ARG 0.019 0.001 ARG I 240 ********************** 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 212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8408 (ttp80) REVERT: D 19 LYS cc_start: 0.9093 (tptp) cc_final: 0.8376 (tppp) REVERT: D 22 GLU cc_start: 0.8376 (pp20) cc_final: 0.8003 (pp20) REVERT: D 23 ASP cc_start: 0.8736 (m-30) cc_final: 0.8147 (m-30) REVERT: D 38 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8813 (mp) REVERT: F 40 ASP cc_start: 0.8468 (t0) cc_final: 0.8045 (t0) REVERT: E 19 LYS cc_start: 0.8621 (mppt) cc_final: 0.7998 (tppp) REVERT: E 22 GLU cc_start: 0.8316 (pp20) cc_final: 0.8010 (pp20) REVERT: E 23 ASP cc_start: 0.8950 (m-30) cc_final: 0.8258 (m-30) REVERT: H 67 PHE cc_start: 0.8827 (t80) cc_final: 0.8470 (t80) REVERT: H 75 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8256 (tm-30) REVERT: H 104 GLU cc_start: 0.8687 (tp30) cc_final: 0.8063 (tp30) REVERT: H 105 LYS cc_start: 0.8986 (tttm) cc_final: 0.8780 (tttp) REVERT: H 107 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8169 (tm-30) REVERT: H 111 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8510 (tm-30) REVERT: H 112 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8594 (pp30) REVERT: C 75 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8353 (tm-30) REVERT: C 102 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: C 104 GLU cc_start: 0.8698 (tp30) cc_final: 0.8085 (tp30) REVERT: C 107 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7970 (tm-30) REVERT: C 112 GLN cc_start: 0.9272 (tt0) cc_final: 0.8965 (tm-30) REVERT: J 9 LYS cc_start: 0.8756 (mptt) cc_final: 0.8487 (mptt) REVERT: J 46 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8149 (mm-30) REVERT: B 76 CYS cc_start: 0.8362 (m) cc_final: 0.8000 (t) REVERT: B 163 GLN cc_start: 0.8256 (mt0) cc_final: 0.7989 (tt0) REVERT: B 195 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8622 (mtm-85) REVERT: I 176 MET cc_start: 0.8050 (mtt) cc_final: 0.7846 (mtm) REVERT: I 293 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8397 (ttm110) outliers start: 16 outliers final: 8 residues processed: 202 average time/residue: 1.3520 time to fit residues: 289.8895 Evaluate side-chains 205 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 E residue 25 ILE Chi-restraints excluded: chain E residue 28 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 195 ARG Chi-restraints excluded: chain I residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.099526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067880 restraints weight = 16436.222| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.53 r_work: 0.2789 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9236 Z= 0.219 Angle : 0.727 9.736 12128 Z= 0.357 Chirality : 0.041 0.189 1182 Planarity : 0.005 0.068 1371 Dihedral : 17.475 89.297 2439 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.62 % Allowed : 24.63 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.28), residues: 931 helix: 3.53 (0.29), residues: 300 sheet: 1.69 (0.26), residues: 388 loop : -0.19 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 259 HIS 0.003 0.001 HIS B 220 PHE 0.023 0.001 PHE H 72 TYR 0.007 0.001 TYR D 34 ARG 0.019 0.001 ARG B 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4804.72 seconds wall clock time: 86 minutes 26.68 seconds (5186.68 seconds total)