Starting phenix.real_space_refine on Fri Nov 15 16:23:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubf_42085/11_2024/8ubf_42085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubf_42085/11_2024/8ubf_42085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubf_42085/11_2024/8ubf_42085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubf_42085/11_2024/8ubf_42085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubf_42085/11_2024/8ubf_42085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubf_42085/11_2024/8ubf_42085.cif" } resolution = 3.61 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= 0.018 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 102 5.49 5 S 36 5.16 5 C 5560 2.51 5 N 1682 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9291 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2593 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 1 Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "H" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "I" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1973 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 34} Link IDs: {'rna2p': 16, 'rna3p': 75} Chain breaks: 2 Time building chain proxies: 6.74, per 1000 atoms: 0.73 Number of scatterers: 9291 At special positions: 0 Unit cell: (85, 87, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 102 15.00 O 1911 8.00 N 1682 7.00 C 5560 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: 2.75 Conformation dependent library (CDL) restraints added in 895.5 milliseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 2 sheets defined 76.2% alpha, 1.8% beta 32 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.558A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.993A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.558A pdb=" N GLY A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.591A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.733A pdb=" N GLN A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 275 through 289 removed outlier: 4.021A pdb=" N ARG A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.892A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.901A pdb=" N TYR A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.748A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 62 removed outlier: 4.269A pdb=" N VAL B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.880A pdb=" N LEU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.880A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.519A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.584A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 32 removed outlier: 3.825A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.560A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.716A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.637A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 32 removed outlier: 4.502A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 removed outlier: 3.523A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.613A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.935A pdb=" N HIS F 92 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA F 93 " --> pdb=" O LYS F 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.293A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.657A pdb=" N HIS A 133 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 252 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265 471 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 2.86 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: 1.18 - 1.31: 1251 1.31 - 1.44: 3278 1.44 - 1.57: 4914 1.57 - 1.70: 201 1.70 - 1.84: 61 Bond restraints: 9705 Sorted by residual: bond pdb=" N LYS D 90 " pdb=" CA LYS D 90 " ideal model delta sigma weight residual 1.463 1.391 0.073 6.90e-03 2.10e+04 1.11e+02 bond pdb=" CA LYS D 90 " pdb=" C LYS D 90 " ideal model delta sigma weight residual 1.521 1.596 -0.075 1.08e-02 8.57e+03 4.85e+01 bond pdb=" C LYS D 90 " pdb=" O LYS D 90 " ideal model delta sigma weight residual 1.244 1.181 0.062 9.10e-03 1.21e+04 4.71e+01 bond pdb=" N ILE C 88 " pdb=" CA ILE C 88 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" CB TRP A 15 " pdb=" CG TRP A 15 " ideal model delta sigma weight residual 1.498 1.418 0.080 3.10e-02 1.04e+03 6.62e+00 ... (remaining 9700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 13178 2.41 - 4.83: 371 4.83 - 7.24: 41 7.24 - 9.66: 12 9.66 - 12.07: 2 Bond angle restraints: 13604 Sorted by residual: angle pdb=" N PRO C 91 " pdb=" CA PRO C 91 " pdb=" CB PRO C 91 " ideal model delta sigma weight residual 103.25 95.59 7.66 1.05e+00 9.07e-01 5.32e+01 angle pdb=" O LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " ideal model delta sigma weight residual 120.27 125.05 -4.78 6.90e-01 2.10e+00 4.81e+01 angle pdb=" CA LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " ideal model delta sigma weight residual 120.58 116.04 4.54 7.40e-01 1.83e+00 3.76e+01 angle pdb=" C LYS D 90 " pdb=" N PRO D 91 " pdb=" CA PRO D 91 " ideal model delta sigma weight residual 119.84 112.38 7.46 1.25e+00 6.40e-01 3.56e+01 angle pdb=" N GLN F 32 " pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 113.18 107.68 5.50 1.21e+00 6.83e-01 2.06e+01 ... (remaining 13599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 5242 35.29 - 70.58: 648 70.58 - 105.87: 55 105.87 - 141.15: 1 141.15 - 176.44: 3 Dihedral angle restraints: 5949 sinusoidal: 3385 harmonic: 2564 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 56.23 175.77 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -87.90 -72.10 1 1.50e+01 4.44e-03 2.96e+01 dihedral pdb=" CA ALA A 163 " pdb=" C ALA A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1477 0.087 - 0.174: 101 0.174 - 0.262: 6 0.262 - 0.349: 2 0.349 - 0.436: 3 Chirality restraints: 1589 Sorted by residual: chirality pdb=" P U H 118 " pdb=" OP1 U H 118 " pdb=" OP2 U H 118 " pdb=" O5' U H 118 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" P U I 7 " pdb=" OP1 U I 7 " pdb=" OP2 U I 7 " pdb=" O5' U I 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE A 181 " pdb=" CA ILE A 181 " pdb=" CG1 ILE A 181 " pdb=" CG2 ILE A 181 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 1586 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.042 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO C 91 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G I 4 " -0.000 2.00e-02 2.50e+03 1.39e-02 5.79e+00 pdb=" N9 G I 4 " -0.038 2.00e-02 2.50e+03 pdb=" C8 G I 4 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G I 4 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G I 4 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G I 4 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G I 4 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G I 4 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G I 4 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G I 4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G I 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G I 4 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " 0.024 2.00e-02 2.50e+03 1.78e-02 5.54e+00 pdb=" CG PHE A 231 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " 0.004 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2729 2.82 - 3.34: 9149 3.34 - 3.86: 18895 3.86 - 4.38: 22753 4.38 - 4.90: 32113 Nonbonded interactions: 85639 Sorted by model distance: nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.341 3.040 nonbonded pdb=" O LYS C 90 " pdb=" C PRO C 91 " model vdw 2.369 3.270 nonbonded pdb=" NE2 HIS B 97 " pdb=" OP1 A H 123 " model vdw 2.419 3.120 nonbonded pdb=" O ALA A 108 " pdb=" N ARG A 110 " model vdw 2.420 3.120 ... (remaining 85634 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 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.600 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.007 0.080 9705 Z= 0.459 Angle : 0.979 12.072 13604 Z= 0.549 Chirality : 0.053 0.436 1589 Planarity : 0.008 0.062 1338 Dihedral : 24.771 176.442 4295 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 3.23 % Allowed : 9.22 % Favored : 87.56 % Rotamer: Outliers : 22.69 % Allowed : 12.64 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.90 (0.23), residues: 868 helix: -1.94 (0.17), residues: 656 sheet: -3.17 (1.11), residues: 18 loop : -4.21 (0.35), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP A 309 HIS 0.023 0.003 HIS C 38 PHE 0.040 0.005 PHE A 231 TYR 0.026 0.005 TYR A 107 ARG 0.010 0.001 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 331 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (ptm160) REVERT: A 14 THR cc_start: 0.7743 (p) cc_final: 0.7498 (p) REVERT: A 63 TYR cc_start: 0.6104 (m-80) cc_final: 0.5053 (m-80) REVERT: A 99 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7845 (tm-30) REVERT: A 102 LEU cc_start: 0.8435 (mt) cc_final: 0.8208 (mp) REVERT: A 110 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7092 (ptm160) REVERT: A 128 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8626 (ttt180) REVERT: A 145 SER cc_start: 0.8724 (m) cc_final: 0.8502 (p) REVERT: A 156 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: A 158 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6661 (mttt) REVERT: A 200 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7562 (mm) REVERT: A 210 TRP cc_start: 0.9149 (p-90) cc_final: 0.8217 (p-90) REVERT: A 226 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (tp30) REVERT: A 258 ILE cc_start: 0.8718 (mp) cc_final: 0.8469 (mp) REVERT: A 319 MET cc_start: 0.7278 (mtp) cc_final: 0.6976 (ptp) REVERT: B 1 MET cc_start: 0.7588 (tmm) cc_final: 0.7367 (tmm) REVERT: B 2 GLU cc_start: 0.8183 (tp30) cc_final: 0.7793 (tp30) REVERT: B 16 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 22 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (ttp-170) REVERT: B 65 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.7411 (p) REVERT: B 80 PHE cc_start: 0.8845 (t80) cc_final: 0.8627 (t80) REVERT: B 105 LEU cc_start: 0.8540 (mt) cc_final: 0.8305 (mp) REVERT: B 113 LEU cc_start: 0.9138 (tp) cc_final: 0.8930 (tt) REVERT: B 115 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9116 (p) REVERT: D 53 VAL cc_start: 0.9239 (t) cc_final: 0.8916 (t) REVERT: D 68 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9067 (mt) REVERT: D 69 TYR cc_start: 0.9126 (m-10) cc_final: 0.8639 (m-80) REVERT: D 77 MET cc_start: 0.8942 (tpt) cc_final: 0.8725 (tpp) REVERT: D 99 VAL cc_start: 0.7994 (t) cc_final: 0.7751 (t) REVERT: D 120 VAL cc_start: 0.8318 (t) cc_final: 0.7815 (m) REVERT: E 43 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: E 56 PHE cc_start: 0.8610 (m-10) cc_final: 0.8342 (m-10) REVERT: E 108 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9081 (tp30) REVERT: F 21 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8509 (tm-30) REVERT: F 22 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8906 (mtm-85) REVERT: F 61 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (tptp) REVERT: F 69 TYR cc_start: 0.8983 (m-80) cc_final: 0.8580 (m-80) outliers start: 167 outliers final: 25 residues processed: 422 average time/residue: 0.3219 time to fit residues: 169.8911 Evaluate side-chains 255 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 61 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 92 ASN A 297 GLN C 92 HIS C 121 ASN D 32 GLN D 89 GLN D 103 GLN E 32 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9705 Z= 0.257 Angle : 0.718 11.301 13604 Z= 0.374 Chirality : 0.042 0.258 1589 Planarity : 0.007 0.140 1338 Dihedral : 22.276 172.075 2675 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.29 % Favored : 90.67 % Rotamer: Outliers : 6.79 % Allowed : 18.48 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.07 (0.29), residues: 868 helix: 0.10 (0.20), residues: 654 sheet: -1.84 (1.07), residues: 20 loop : -3.22 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 116 HIS 0.004 0.001 HIS B 38 PHE 0.043 0.003 PHE C 80 TYR 0.027 0.002 TYR B 69 ARG 0.007 0.001 ARG E 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7578 (tm-30) REVERT: A 102 LEU cc_start: 0.8223 (mt) cc_final: 0.7921 (mp) REVERT: A 107 TYR cc_start: 0.8526 (m-80) cc_final: 0.8289 (m-80) REVERT: A 128 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8797 (ttp-110) REVERT: A 145 SER cc_start: 0.8877 (m) cc_final: 0.8668 (p) REVERT: A 158 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6833 (mttt) REVERT: A 303 TRP cc_start: 0.8118 (t60) cc_final: 0.7774 (t60) REVERT: B 2 GLU cc_start: 0.7997 (tp30) cc_final: 0.7592 (pp20) REVERT: B 16 ILE cc_start: 0.9144 (tt) cc_final: 0.8887 (tt) REVERT: B 105 LEU cc_start: 0.8440 (mt) cc_final: 0.8228 (mp) REVERT: C 18 GLU cc_start: 0.8682 (tp30) cc_final: 0.8472 (tp30) REVERT: C 88 ILE cc_start: 0.7107 (pt) cc_final: 0.6832 (pt) REVERT: C 100 GLU cc_start: 0.7067 (tt0) cc_final: 0.6768 (tt0) REVERT: D 43 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7718 (tt0) REVERT: D 65 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8537 (t) REVERT: D 69 TYR cc_start: 0.9136 (m-10) cc_final: 0.8767 (m-80) REVERT: D 75 LEU cc_start: 0.8849 (mt) cc_final: 0.8491 (tp) REVERT: E 65 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8625 (t) REVERT: F 13 GLN cc_start: 0.6858 (mp10) cc_final: 0.6487 (mp10) REVERT: F 69 TYR cc_start: 0.8978 (m-80) cc_final: 0.8252 (m-80) REVERT: F 90 LYS cc_start: 0.7272 (tptt) cc_final: 0.7054 (tppt) outliers start: 50 outliers final: 18 residues processed: 288 average time/residue: 0.2732 time to fit residues: 103.0578 Evaluate side-chains 230 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN D 98 GLN D 103 GLN E 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9705 Z= 0.212 Angle : 0.658 8.308 13604 Z= 0.338 Chirality : 0.040 0.196 1589 Planarity : 0.006 0.121 1338 Dihedral : 21.569 178.843 2599 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.26 % Favored : 92.05 % Rotamer: Outliers : 4.89 % Allowed : 22.42 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 868 helix: 0.60 (0.20), residues: 649 sheet: 0.13 (1.30), residues: 18 loop : -2.74 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 116 HIS 0.004 0.001 HIS A 328 PHE 0.049 0.003 PHE C 80 TYR 0.013 0.002 TYR F 26 ARG 0.008 0.001 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.8092 (mt) cc_final: 0.7883 (mp) REVERT: A 128 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8770 (ptp90) REVERT: A 158 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6900 (mttt) REVERT: A 210 TRP cc_start: 0.9163 (p-90) cc_final: 0.8164 (p-90) REVERT: A 256 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7182 (mtp85) REVERT: B 2 GLU cc_start: 0.8073 (tp30) cc_final: 0.7631 (pp20) REVERT: B 16 ILE cc_start: 0.9128 (tt) cc_final: 0.8901 (tt) REVERT: B 63 ASN cc_start: 0.9021 (p0) cc_final: 0.8776 (p0) REVERT: B 105 LEU cc_start: 0.8399 (mt) cc_final: 0.8199 (mp) REVERT: B 113 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8935 (tt) REVERT: C 92 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7752 (t-90) REVERT: C 108 GLU cc_start: 0.8094 (tp30) cc_final: 0.7734 (tp30) REVERT: D 43 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7632 (tt0) REVERT: D 64 GLN cc_start: 0.6758 (tp-100) cc_final: 0.6542 (tp-100) REVERT: D 65 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8487 (t) REVERT: D 68 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9018 (mt) REVERT: D 69 TYR cc_start: 0.9121 (m-10) cc_final: 0.8733 (m-80) REVERT: D 77 MET cc_start: 0.8382 (tpp) cc_final: 0.8169 (tpp) REVERT: D 120 VAL cc_start: 0.7975 (t) cc_final: 0.7480 (m) REVERT: E 13 GLN cc_start: 0.7520 (pm20) cc_final: 0.6897 (tt0) REVERT: E 19 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8414 (tpp80) REVERT: E 108 GLU cc_start: 0.9272 (tp30) cc_final: 0.8982 (tp30) REVERT: F 13 GLN cc_start: 0.7462 (mp10) cc_final: 0.6651 (mp10) REVERT: F 14 MET cc_start: 0.7904 (mmp) cc_final: 0.7227 (tmm) REVERT: F 43 GLU cc_start: 0.8387 (tt0) cc_final: 0.8011 (tm-30) REVERT: F 90 LYS cc_start: 0.7307 (tptt) cc_final: 0.7069 (tptt) REVERT: F 108 GLU cc_start: 0.9121 (tp30) cc_final: 0.8521 (tm-30) outliers start: 36 outliers final: 16 residues processed: 256 average time/residue: 0.2632 time to fit residues: 88.1592 Evaluate side-chains 228 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 52 GLN D 98 GLN E 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 9705 Z= 0.407 Angle : 0.733 9.509 13604 Z= 0.376 Chirality : 0.042 0.201 1589 Planarity : 0.006 0.113 1338 Dihedral : 21.519 178.130 2591 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.72 % Favored : 91.59 % Rotamer: Outliers : 5.03 % Allowed : 23.51 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.29), residues: 868 helix: 0.40 (0.20), residues: 652 sheet: -0.23 (1.29), residues: 20 loop : -2.44 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 116 HIS 0.008 0.001 HIS A 328 PHE 0.048 0.003 PHE C 80 TYR 0.021 0.002 TYR F 28 ARG 0.008 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.8275 (mt) cc_final: 0.8056 (mp) REVERT: A 128 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8806 (ptp90) REVERT: A 256 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7159 (mtp85) REVERT: A 283 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6831 (mmpt) REVERT: B 2 GLU cc_start: 0.8084 (tp30) cc_final: 0.7786 (pm20) REVERT: B 79 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7336 (mtt-85) REVERT: B 105 LEU cc_start: 0.8374 (mt) cc_final: 0.8103 (mp) REVERT: C 92 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7763 (t-90) REVERT: C 108 GLU cc_start: 0.8153 (tp30) cc_final: 0.7802 (tp30) REVERT: D 44 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7971 (mtm) REVERT: D 65 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8637 (t) REVERT: D 69 TYR cc_start: 0.9149 (m-10) cc_final: 0.8730 (m-80) REVERT: E 13 GLN cc_start: 0.7725 (pm20) cc_final: 0.6881 (tt0) REVERT: E 26 TYR cc_start: 0.7725 (t80) cc_final: 0.7494 (t80) REVERT: E 85 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8484 (mm) REVERT: F 13 GLN cc_start: 0.7429 (mp10) cc_final: 0.6727 (mp10) REVERT: F 14 MET cc_start: 0.7766 (mmp) cc_final: 0.7067 (tmm) REVERT: F 68 LEU cc_start: 0.9341 (tp) cc_final: 0.8993 (pp) REVERT: F 69 TYR cc_start: 0.9089 (m-80) cc_final: 0.8312 (m-80) outliers start: 37 outliers final: 16 residues processed: 234 average time/residue: 0.2884 time to fit residues: 86.6159 Evaluate side-chains 216 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 57 ASN A 87 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 64 GLN D 52 GLN D 98 GLN E 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9705 Z= 0.228 Angle : 0.660 8.526 13604 Z= 0.337 Chirality : 0.038 0.193 1589 Planarity : 0.006 0.112 1338 Dihedral : 21.239 179.587 2583 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.91 % Favored : 92.63 % Rotamer: Outliers : 4.35 % Allowed : 24.73 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 868 helix: 0.59 (0.20), residues: 654 sheet: 0.34 (1.37), residues: 20 loop : -2.41 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 303 HIS 0.007 0.001 HIS A 328 PHE 0.029 0.003 PHE B 80 TYR 0.013 0.001 TYR F 28 ARG 0.010 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8494 (m-30) cc_final: 0.7611 (m-30) REVERT: A 128 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8838 (ptp90) REVERT: A 135 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7139 (tp) REVERT: A 210 TRP cc_start: 0.9169 (p-90) cc_final: 0.8169 (p-90) REVERT: A 256 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7277 (mtp85) REVERT: A 283 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6890 (mmpt) REVERT: B 2 GLU cc_start: 0.8145 (tp30) cc_final: 0.7815 (pm20) REVERT: B 5 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8005 (pp20) REVERT: B 44 MET cc_start: 0.8017 (mtp) cc_final: 0.7528 (mpp) REVERT: B 92 HIS cc_start: 0.7836 (p-80) cc_final: 0.7516 (p-80) REVERT: C 92 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7844 (t-90) REVERT: C 108 GLU cc_start: 0.8051 (tp30) cc_final: 0.7717 (tp30) REVERT: D 43 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7750 (tt0) REVERT: D 64 GLN cc_start: 0.6868 (tp40) cc_final: 0.6638 (tp40) REVERT: E 13 GLN cc_start: 0.7688 (pm20) cc_final: 0.7146 (tt0) REVERT: E 26 TYR cc_start: 0.7798 (t80) cc_final: 0.7566 (t80) REVERT: F 13 GLN cc_start: 0.7730 (mp10) cc_final: 0.7046 (mp10) REVERT: F 14 MET cc_start: 0.7656 (mmp) cc_final: 0.7159 (tmm) REVERT: F 43 GLU cc_start: 0.8415 (tt0) cc_final: 0.8082 (tm-30) REVERT: F 68 LEU cc_start: 0.9346 (tp) cc_final: 0.9058 (pp) REVERT: F 69 TYR cc_start: 0.9009 (m-80) cc_final: 0.8231 (m-80) outliers start: 32 outliers final: 19 residues processed: 234 average time/residue: 0.2704 time to fit residues: 82.4055 Evaluate side-chains 221 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 98 GLN D 103 GLN E 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9705 Z= 0.230 Angle : 0.648 9.943 13604 Z= 0.331 Chirality : 0.038 0.186 1589 Planarity : 0.006 0.112 1338 Dihedral : 21.057 178.899 2582 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.14 % Favored : 92.40 % Rotamer: Outliers : 5.16 % Allowed : 24.18 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.29), residues: 868 helix: 0.57 (0.20), residues: 660 sheet: 0.29 (1.31), residues: 20 loop : -2.53 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 303 HIS 0.007 0.001 HIS A 5 PHE 0.029 0.003 PHE C 80 TYR 0.022 0.002 TYR E 20 ARG 0.012 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8557 (m-30) cc_final: 0.7634 (m-30) REVERT: A 135 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7044 (tp) REVERT: A 210 TRP cc_start: 0.9148 (p-90) cc_final: 0.8763 (p-90) REVERT: A 256 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7313 (mtp85) REVERT: A 283 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6797 (mmpt) REVERT: B 2 GLU cc_start: 0.8094 (tp30) cc_final: 0.7807 (pm20) REVERT: B 5 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8031 (pp20) REVERT: B 79 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7339 (mtt-85) REVERT: B 92 HIS cc_start: 0.7931 (p-80) cc_final: 0.7711 (p-80) REVERT: B 119 ARG cc_start: 0.8936 (ttp-110) cc_final: 0.8670 (tpm170) REVERT: C 92 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.8023 (t-90) REVERT: C 108 GLU cc_start: 0.7974 (tp30) cc_final: 0.7671 (tp30) REVERT: D 43 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7735 (tt0) REVERT: D 44 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7848 (mtm) REVERT: D 69 TYR cc_start: 0.9105 (m-10) cc_final: 0.8689 (m-80) REVERT: E 13 GLN cc_start: 0.7871 (pm20) cc_final: 0.7325 (tt0) REVERT: F 13 GLN cc_start: 0.7550 (mp10) cc_final: 0.6774 (mt0) REVERT: F 14 MET cc_start: 0.7790 (mmp) cc_final: 0.7279 (tmm) REVERT: F 43 GLU cc_start: 0.8443 (tt0) cc_final: 0.8108 (tm-30) REVERT: F 68 LEU cc_start: 0.9343 (tp) cc_final: 0.9035 (pp) REVERT: F 69 TYR cc_start: 0.8990 (m-80) cc_final: 0.8201 (m-80) outliers start: 38 outliers final: 20 residues processed: 234 average time/residue: 0.2777 time to fit residues: 84.9860 Evaluate side-chains 222 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN D 52 GLN D 98 GLN E 32 GLN E 38 HIS E 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9705 Z= 0.228 Angle : 0.654 9.969 13604 Z= 0.333 Chirality : 0.038 0.180 1589 Planarity : 0.006 0.113 1338 Dihedral : 20.905 178.402 2578 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.91 % Favored : 92.63 % Rotamer: Outliers : 4.62 % Allowed : 25.54 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 868 helix: 0.61 (0.20), residues: 658 sheet: 1.36 (1.30), residues: 18 loop : -2.27 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 303 HIS 0.006 0.001 HIS A 5 PHE 0.024 0.002 PHE A 287 TYR 0.011 0.001 TYR F 28 ARG 0.013 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8524 (m-30) cc_final: 0.7787 (m-30) REVERT: A 135 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7017 (tp) REVERT: A 210 TRP cc_start: 0.9130 (p-90) cc_final: 0.8694 (p-90) REVERT: A 256 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7348 (mtp85) REVERT: A 283 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6692 (mmpt) REVERT: B 2 GLU cc_start: 0.8129 (tp30) cc_final: 0.7676 (pp20) REVERT: B 5 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8087 (pp20) REVERT: B 79 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7386 (mtt-85) REVERT: B 92 HIS cc_start: 0.7947 (p-80) cc_final: 0.7649 (p90) REVERT: C 92 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.8031 (t-90) REVERT: C 108 GLU cc_start: 0.7918 (tp30) cc_final: 0.7659 (tp30) REVERT: D 43 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7724 (tt0) REVERT: E 13 GLN cc_start: 0.7870 (pm20) cc_final: 0.7328 (tt0) REVERT: F 13 GLN cc_start: 0.7581 (mp10) cc_final: 0.6821 (mt0) REVERT: F 14 MET cc_start: 0.7778 (mmp) cc_final: 0.7348 (tmm) REVERT: F 43 GLU cc_start: 0.8467 (tt0) cc_final: 0.8119 (tm-30) REVERT: F 68 LEU cc_start: 0.9350 (tp) cc_final: 0.9042 (pp) REVERT: F 69 TYR cc_start: 0.9003 (m-80) cc_final: 0.8222 (m-80) outliers start: 34 outliers final: 19 residues processed: 236 average time/residue: 0.2756 time to fit residues: 84.1168 Evaluate side-chains 221 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.0570 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN C 98 GLN C 121 ASN D 32 GLN D 52 GLN D 98 GLN E 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9705 Z= 0.240 Angle : 0.689 12.974 13604 Z= 0.349 Chirality : 0.039 0.181 1589 Planarity : 0.006 0.114 1338 Dihedral : 20.826 178.271 2578 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.68 % Favored : 92.86 % Rotamer: Outliers : 3.67 % Allowed : 26.09 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 868 helix: 0.56 (0.20), residues: 662 sheet: 1.59 (1.32), residues: 18 loop : -2.21 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 303 HIS 0.006 0.001 HIS A 5 PHE 0.032 0.003 PHE C 80 TYR 0.025 0.002 TYR E 20 ARG 0.013 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8553 (m-30) cc_final: 0.7798 (m-30) REVERT: A 135 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7017 (tp) REVERT: A 210 TRP cc_start: 0.9124 (p-90) cc_final: 0.8716 (p-90) REVERT: A 283 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6547 (mmpt) REVERT: B 2 GLU cc_start: 0.8152 (tp30) cc_final: 0.7852 (pm20) REVERT: B 5 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8112 (pp20) REVERT: B 79 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7381 (mtt-85) REVERT: B 92 HIS cc_start: 0.7859 (p-80) cc_final: 0.7554 (p90) REVERT: B 119 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8463 (tpp-160) REVERT: C 92 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.8054 (t-90) REVERT: C 108 GLU cc_start: 0.7940 (tp30) cc_final: 0.7663 (tp30) REVERT: D 13 GLN cc_start: 0.5492 (mt0) cc_final: 0.5038 (mt0) REVERT: D 44 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7842 (mtm) REVERT: E 13 GLN cc_start: 0.7906 (pm20) cc_final: 0.7337 (tt0) REVERT: F 13 GLN cc_start: 0.7676 (mp10) cc_final: 0.6998 (mt0) REVERT: F 14 MET cc_start: 0.7854 (mmp) cc_final: 0.7393 (tmm) REVERT: F 43 GLU cc_start: 0.8443 (tt0) cc_final: 0.8082 (tm-30) REVERT: F 68 LEU cc_start: 0.9344 (tp) cc_final: 0.9051 (pp) REVERT: F 69 TYR cc_start: 0.9029 (m-80) cc_final: 0.8264 (m-80) outliers start: 27 outliers final: 19 residues processed: 227 average time/residue: 0.2682 time to fit residues: 79.4300 Evaluate side-chains 224 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 123 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 64 GLN C 121 ASN D 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9705 Z= 0.253 Angle : 0.697 11.741 13604 Z= 0.356 Chirality : 0.040 0.237 1589 Planarity : 0.007 0.115 1338 Dihedral : 20.795 178.203 2578 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.60 % Favored : 92.05 % Rotamer: Outliers : 3.26 % Allowed : 25.00 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.29), residues: 868 helix: 0.58 (0.20), residues: 661 sheet: 1.87 (1.34), residues: 18 loop : -2.12 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 303 HIS 0.006 0.001 HIS A 5 PHE 0.030 0.003 PHE B 80 TYR 0.027 0.002 TYR E 20 ARG 0.018 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8561 (m-30) cc_final: 0.7807 (m-30) REVERT: A 135 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7033 (tp) REVERT: A 210 TRP cc_start: 0.9133 (p-90) cc_final: 0.8704 (p-90) REVERT: A 283 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6407 (mmpt) REVERT: B 2 GLU cc_start: 0.8145 (tp30) cc_final: 0.7834 (pm20) REVERT: B 5 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: B 44 MET cc_start: 0.7987 (mtp) cc_final: 0.7536 (mpp) REVERT: B 79 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7396 (mtt-85) REVERT: B 92 HIS cc_start: 0.7929 (p-80) cc_final: 0.7622 (p90) REVERT: B 119 ARG cc_start: 0.8826 (ttm110) cc_final: 0.8553 (tpp-160) REVERT: C 92 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8154 (t-90) REVERT: C 108 GLU cc_start: 0.7926 (tp30) cc_final: 0.7617 (tp30) REVERT: D 13 GLN cc_start: 0.5390 (mt0) cc_final: 0.4938 (mt0) REVERT: D 44 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7820 (mtm) REVERT: D 69 TYR cc_start: 0.9000 (m-10) cc_final: 0.8678 (m-10) REVERT: E 13 GLN cc_start: 0.7970 (pm20) cc_final: 0.7430 (tt0) REVERT: F 13 GLN cc_start: 0.7802 (mp10) cc_final: 0.7161 (mt0) REVERT: F 14 MET cc_start: 0.7823 (mmp) cc_final: 0.7365 (tmm) REVERT: F 43 GLU cc_start: 0.8461 (tt0) cc_final: 0.8089 (tm-30) REVERT: F 68 LEU cc_start: 0.9331 (tp) cc_final: 0.9036 (pp) REVERT: F 69 TYR cc_start: 0.9037 (m-80) cc_final: 0.8257 (m-80) outliers start: 24 outliers final: 16 residues processed: 225 average time/residue: 0.2558 time to fit residues: 75.9099 Evaluate side-chains 221 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN C 121 ASN D 52 GLN D 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9705 Z= 0.256 Angle : 0.715 11.923 13604 Z= 0.364 Chirality : 0.040 0.240 1589 Planarity : 0.007 0.116 1338 Dihedral : 20.791 177.950 2578 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.26 % Favored : 92.40 % Rotamer: Outliers : 2.72 % Allowed : 26.49 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 868 helix: 0.50 (0.20), residues: 664 sheet: 2.26 (1.37), residues: 18 loop : -2.09 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 303 HIS 0.005 0.001 HIS A 5 PHE 0.030 0.003 PHE A 287 TYR 0.023 0.002 TYR E 20 ARG 0.016 0.001 ARG D 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8558 (m-30) cc_final: 0.8280 (m-30) REVERT: A 135 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6989 (tp) REVERT: A 210 TRP cc_start: 0.9128 (p-90) cc_final: 0.8687 (p-90) REVERT: A 283 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.6417 (mmpt) REVERT: B 2 GLU cc_start: 0.8158 (tp30) cc_final: 0.7841 (pm20) REVERT: B 5 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: B 44 MET cc_start: 0.7996 (mtp) cc_final: 0.7540 (mpp) REVERT: B 79 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7402 (mtt-85) REVERT: B 92 HIS cc_start: 0.7964 (p-80) cc_final: 0.7655 (p90) REVERT: B 119 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8532 (tpp-160) REVERT: C 92 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.8425 (t-90) REVERT: C 108 GLU cc_start: 0.7895 (tp30) cc_final: 0.7578 (tp30) REVERT: D 44 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7814 (mtm) REVERT: D 69 TYR cc_start: 0.8968 (m-10) cc_final: 0.8642 (m-10) REVERT: E 13 GLN cc_start: 0.7945 (pm20) cc_final: 0.7359 (tt0) REVERT: E 18 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8587 (mp0) REVERT: F 13 GLN cc_start: 0.7822 (mp10) cc_final: 0.7228 (mt0) REVERT: F 14 MET cc_start: 0.7808 (mmp) cc_final: 0.7340 (tmm) REVERT: F 43 GLU cc_start: 0.8448 (tt0) cc_final: 0.8088 (tm-30) REVERT: F 68 LEU cc_start: 0.9332 (tp) cc_final: 0.9084 (pp) REVERT: F 69 TYR cc_start: 0.9033 (m-80) cc_final: 0.8392 (m-80) REVERT: F 90 LYS cc_start: 0.7401 (tptt) cc_final: 0.6984 (tptp) outliers start: 20 outliers final: 15 residues processed: 221 average time/residue: 0.2524 time to fit residues: 74.4324 Evaluate side-chains 218 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 67 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 27 HIS A 57 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN C 121 ASN D 13 GLN D 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.144492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.110551 restraints weight = 20391.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113525 restraints weight = 12667.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115382 restraints weight = 9687.750| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9705 Z= 0.234 Angle : 0.709 11.527 13604 Z= 0.361 Chirality : 0.040 0.250 1589 Planarity : 0.006 0.114 1338 Dihedral : 20.753 176.121 2578 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.26 % Favored : 92.51 % Rotamer: Outliers : 2.99 % Allowed : 26.90 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 868 helix: 0.47 (0.20), residues: 664 sheet: 2.26 (1.28), residues: 18 loop : -2.14 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 303 HIS 0.007 0.001 HIS D 38 PHE 0.030 0.003 PHE C 80 TYR 0.022 0.002 TYR E 20 ARG 0.014 0.001 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.15 seconds wall clock time: 44 minutes 41.55 seconds (2681.55 seconds total)