Starting phenix.real_space_refine on Tue Feb 13 16:29:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/02_2024/7xn6_33312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/02_2024/7xn6_33312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/02_2024/7xn6_33312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/02_2024/7xn6_33312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/02_2024/7xn6_33312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/02_2024/7xn6_33312_updated.pdb" } resolution = 3.45 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= 1.000 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 2 5.49 5 S 38 5.16 5 C 4346 2.51 5 N 1211 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 190": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1714 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1394 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 5 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.12, per 1000 atoms: 0.60 Number of scatterers: 6874 At special positions: 0 Unit cell: (107.776, 96.83, 76.622, 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 38 16.00 P 2 15.00 O 1277 8.00 N 1211 7.00 C 4346 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 7 sheets defined 35.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.671A pdb=" N LEU A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 136 through 143 removed outlier: 4.550A pdb=" N ASN A 141 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A 142 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 removed outlier: 4.355A pdb=" N CYS A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'B' and resid 51 through 73 removed outlier: 4.988A pdb=" N ALA B 57 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG B 60 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 65 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 69 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B 71 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 93 through 113 removed outlier: 4.450A pdb=" N ARG B 98 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA B 109 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 113 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 252 through 255 No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.594A pdb=" N GLU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 4.043A pdb=" N ALA B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 321 removed outlier: 3.800A pdb=" N SER B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.821A pdb=" N GLY B 361 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 4.148A pdb=" N THR B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 410 through 413 No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 421 through 430 Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'C' and resid 69 through 79 removed outlier: 3.783A pdb=" N GLU C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 137 through 143 removed outlier: 5.150A pdb=" N PHE C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 103 through 111 removed outlier: 3.628A pdb=" N THR D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 127 removed outlier: 4.042A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 8.394A pdb=" N LYS A 88 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 49 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 46 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N CYS A 116 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 157 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 118 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 159 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 194 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= C, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= D, first strand: chain 'B' and resid 149 through 152 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 184 Processing sheet with id= F, first strand: chain 'B' and resid 211 through 213 Processing sheet with id= G, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.521A pdb=" N VAL C 115 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 48 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 157 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU C 118 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 159 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 194 " --> pdb=" O LYS C 156 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1150 1.29 - 1.42: 1879 1.42 - 1.55: 3918 1.55 - 1.68: 6 1.68 - 1.81: 64 Bond restraints: 7017 Sorted by residual: bond pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 1.397 1.573 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 1.522 1.413 0.109 1.34e-02 5.57e+03 6.65e+01 bond pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " ideal model delta sigma weight residual 1.529 1.675 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" CA ALA B 141 " pdb=" C ALA B 141 " ideal model delta sigma weight residual 1.528 1.449 0.080 1.39e-02 5.18e+03 3.28e+01 bond pdb=" CA SER B 139 " pdb=" C SER B 139 " ideal model delta sigma weight residual 1.522 1.453 0.070 1.23e-02 6.61e+03 3.20e+01 ... (remaining 7012 not shown) Histogram of bond angle deviations from ideal: 87.63 - 97.30: 2 97.30 - 106.96: 187 106.96 - 116.63: 4523 116.63 - 126.29: 4642 126.29 - 135.96: 93 Bond angle restraints: 9447 Sorted by residual: angle pdb=" O3A APR A1001 " pdb=" PB APR A1001 " pdb=" O5D APR A1001 " ideal model delta sigma weight residual 101.31 124.38 -23.07 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 110.00 87.63 22.37 3.00e+00 1.11e-01 5.56e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 113.38 105.51 7.87 1.23e+00 6.61e-01 4.09e+01 angle pdb=" C5D APR A1001 " pdb=" C4D APR A1001 " pdb=" O4D APR A1001 " ideal model delta sigma weight residual 111.97 130.75 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" O3A APR A1001 " pdb=" PA APR A1001 " pdb=" O5' APR A1001 " ideal model delta sigma weight residual 102.36 121.10 -18.74 3.00e+00 1.11e-01 3.90e+01 ... (remaining 9442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3681 17.82 - 35.64: 426 35.64 - 53.46: 89 53.46 - 71.28: 11 71.28 - 89.09: 10 Dihedral angle restraints: 4217 sinusoidal: 1729 harmonic: 2488 Sorted by residual: dihedral pdb=" CA GLU D 140 " pdb=" C GLU D 140 " pdb=" N PHE D 141 " pdb=" CA PHE D 141 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LYS B 300 " pdb=" C LYS B 300 " pdb=" N ALA B 301 " pdb=" CA ALA B 301 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C ASN B 355 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta harmonic sigma weight residual -122.60 -110.04 -12.56 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 4214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 1002 0.185 - 0.370: 5 0.370 - 0.556: 1 0.556 - 0.741: 0 0.741 - 0.926: 2 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C2D APR A1001 " pdb=" C1D APR A1001 " pdb=" C3D APR A1001 " pdb=" O2D APR A1001 " both_signs ideal model delta sigma weight residual False -2.45 -3.38 0.93 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C3D APR A1001 " pdb=" C2D APR A1001 " pdb=" C4D APR A1001 " pdb=" O3D APR A1001 " both_signs ideal model delta sigma weight residual False -2.71 -1.96 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C4D APR A1001 " pdb=" C3D APR A1001 " pdb=" C5D APR A1001 " pdb=" O4D APR A1001 " both_signs ideal model delta sigma weight residual False -2.49 -2.04 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 1007 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' APR A1001 " -0.124 2.00e-02 2.50e+03 5.80e-02 9.25e+01 pdb=" C2 APR A1001 " 0.007 2.00e-02 2.50e+03 pdb=" C4 APR A1001 " 0.060 2.00e-02 2.50e+03 pdb=" C5 APR A1001 " 0.057 2.00e-02 2.50e+03 pdb=" C6 APR A1001 " -0.001 2.00e-02 2.50e+03 pdb=" C8 APR A1001 " 0.016 2.00e-02 2.50e+03 pdb=" N1 APR A1001 " -0.024 2.00e-02 2.50e+03 pdb=" N3 APR A1001 " 0.051 2.00e-02 2.50e+03 pdb=" N6 APR A1001 " -0.095 2.00e-02 2.50e+03 pdb=" N7 APR A1001 " 0.046 2.00e-02 2.50e+03 pdb=" N9 APR A1001 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 66 " 0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLN B 66 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN B 66 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 67 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 443 " -0.016 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C ASN B 443 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN B 443 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 444 " -0.018 2.00e-02 2.50e+03 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 4 2.26 - 2.92: 2885 2.92 - 3.58: 9423 3.58 - 4.24: 15292 4.24 - 4.90: 26023 Nonbonded interactions: 53627 Sorted by model distance: nonbonded pdb=" NE ARG A 207 " pdb=" C1D APR A1001 " model vdw 1.596 3.550 nonbonded pdb=" C3D APR A1001 " pdb=" O5D APR A1001 " model vdw 2.029 2.776 nonbonded pdb=" CZ ARG A 207 " pdb=" C1D APR A1001 " model vdw 2.227 2.960 nonbonded pdb=" OH TYR A 37 " pdb=" O GLY A 153 " model vdw 2.238 2.440 nonbonded pdb=" O PHE B 72 " pdb=" N LEU B 85 " model vdw 2.261 2.520 ... (remaining 53622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.120 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: 10.210 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.000 Find NCS groups from input model: 0.190 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.176 7017 Z= 0.455 Angle : 0.965 23.071 9447 Z= 0.518 Chirality : 0.061 0.926 1010 Planarity : 0.006 0.069 1221 Dihedral : 15.940 89.095 2611 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.70 % Allowed : 0.98 % Favored : 98.33 % Cbeta Deviations : 0.25 % 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: -3.19 (0.27), residues: 839 helix: -0.96 (0.28), residues: 342 sheet: -2.81 (0.47), residues: 119 loop : -2.98 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 261 HIS 0.007 0.001 HIS A 121 PHE 0.007 0.001 PHE A 78 TYR 0.016 0.001 TYR B 68 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: B 306 GLN cc_start: 0.6926 (pp30) cc_final: 0.6716 (pp30) REVERT: B 332 MET cc_start: 0.8470 (tmm) cc_final: 0.8254 (tmm) REVERT: C 89 ASN cc_start: 0.7856 (p0) cc_final: 0.7637 (p0) REVERT: C 102 ASP cc_start: 0.7464 (m-30) cc_final: 0.6305 (m-30) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.1964 time to fit residues: 35.3968 Evaluate side-chains 106 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain B residue 139 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 121 HIS A 208 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN B 210 ASN B 443 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7017 Z= 0.201 Angle : 0.565 5.795 9447 Z= 0.301 Chirality : 0.042 0.193 1010 Planarity : 0.005 0.066 1221 Dihedral : 7.974 79.758 986 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.23 % Allowed : 8.65 % Favored : 89.12 % 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: -3.01 (0.27), residues: 839 helix: -0.93 (0.27), residues: 336 sheet: -2.78 (0.46), residues: 122 loop : -2.69 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.029 0.001 PHE A 247 TYR 0.018 0.001 TYR A 37 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4817 (OUTLIER) cc_final: 0.4311 (m100) REVERT: C 89 ASN cc_start: 0.7967 (p0) cc_final: 0.7742 (p0) outliers start: 16 outliers final: 14 residues processed: 118 average time/residue: 0.1880 time to fit residues: 29.7305 Evaluate side-chains 122 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 107 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7017 Z= 0.229 Angle : 0.566 7.054 9447 Z= 0.299 Chirality : 0.042 0.139 1010 Planarity : 0.005 0.062 1221 Dihedral : 7.713 79.481 985 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.23 % Allowed : 12.97 % Favored : 84.80 % 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: -2.93 (0.28), residues: 839 helix: -1.02 (0.27), residues: 345 sheet: -2.65 (0.46), residues: 122 loop : -2.55 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.010 0.001 PHE B 299 TYR 0.020 0.001 TYR A 37 ARG 0.003 0.000 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4684 (OUTLIER) cc_final: 0.4179 (m100) REVERT: C 89 ASN cc_start: 0.7989 (p0) cc_final: 0.7725 (p0) REVERT: D 140 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6988 (mm-30) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.2031 time to fit residues: 29.4652 Evaluate side-chains 111 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 51 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7017 Z= 0.134 Angle : 0.504 6.810 9447 Z= 0.267 Chirality : 0.040 0.136 1010 Planarity : 0.004 0.054 1221 Dihedral : 7.201 76.091 985 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.23 % Allowed : 14.23 % Favored : 83.54 % 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: -2.77 (0.28), residues: 839 helix: -0.87 (0.28), residues: 359 sheet: -2.41 (0.47), residues: 122 loop : -2.59 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.004 0.001 HIS B 327 PHE 0.011 0.001 PHE A 247 TYR 0.016 0.001 TYR A 37 ARG 0.002 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4558 (OUTLIER) cc_final: 0.4086 (m100) REVERT: C 89 ASN cc_start: 0.8033 (p0) cc_final: 0.7757 (p0) REVERT: C 190 GLU cc_start: 0.7175 (tp30) cc_final: 0.6972 (tp30) REVERT: D 110 THR cc_start: 0.7141 (p) cc_final: 0.6878 (p) REVERT: D 140 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6855 (mm-30) outliers start: 16 outliers final: 13 residues processed: 110 average time/residue: 0.2076 time to fit residues: 31.0394 Evaluate side-chains 113 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.6484 ------------------------------------------------------------------------------- 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: 0.7914 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7017 Z= 0.358 Angle : 0.608 8.924 9447 Z= 0.316 Chirality : 0.044 0.158 1010 Planarity : 0.005 0.053 1221 Dihedral : 7.757 75.636 985 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.21 % Allowed : 14.64 % Favored : 82.15 % 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: -2.86 (0.28), residues: 839 helix: -0.99 (0.27), residues: 349 sheet: -2.60 (0.46), residues: 122 loop : -2.50 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 261 HIS 0.018 0.002 HIS A 121 PHE 0.013 0.002 PHE B 78 TYR 0.023 0.002 TYR A 37 ARG 0.003 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8091 (p0) cc_final: 0.7353 (p0) REVERT: A 229 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8414 (mmmt) REVERT: B 233 PHE cc_start: 0.6472 (m-80) cc_final: 0.6219 (m-80) REVERT: C 89 ASN cc_start: 0.8039 (p0) cc_final: 0.7750 (p0) REVERT: C 262 ILE cc_start: 0.8108 (mp) cc_final: 0.7824 (mm) REVERT: D 110 THR cc_start: 0.7128 (p) cc_final: 0.6851 (p) REVERT: D 140 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6970 (mm-30) outliers start: 23 outliers final: 18 residues processed: 115 average time/residue: 0.1894 time to fit residues: 29.6438 Evaluate side-chains 118 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7017 Z= 0.192 Angle : 0.540 7.629 9447 Z= 0.283 Chirality : 0.041 0.196 1010 Planarity : 0.004 0.056 1221 Dihedral : 7.512 72.590 985 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.51 % Allowed : 17.29 % Favored : 80.20 % 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: -2.85 (0.28), residues: 839 helix: -0.98 (0.27), residues: 366 sheet: -2.48 (0.46), residues: 122 loop : -2.58 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 261 HIS 0.005 0.001 HIS C 234 PHE 0.011 0.001 PHE B 58 TYR 0.018 0.001 TYR A 37 ARG 0.002 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 229 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8339 (pttm) REVERT: C 89 ASN cc_start: 0.7990 (p0) cc_final: 0.7704 (p0) REVERT: C 262 ILE cc_start: 0.8062 (mp) cc_final: 0.7823 (mm) REVERT: D 110 THR cc_start: 0.7192 (p) cc_final: 0.6963 (p) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.1759 time to fit residues: 24.5929 Evaluate side-chains 107 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.0770 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 overall best weight: 0.5954 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7017 Z= 0.175 Angle : 0.525 8.648 9447 Z= 0.274 Chirality : 0.041 0.166 1010 Planarity : 0.004 0.054 1221 Dihedral : 7.357 68.656 985 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.79 % Allowed : 16.88 % Favored : 80.33 % 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: -2.66 (0.29), residues: 839 helix: -0.80 (0.28), residues: 360 sheet: -2.41 (0.46), residues: 122 loop : -2.48 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.008 0.001 PHE A 78 TYR 0.008 0.001 TYR B 225 ARG 0.003 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 229 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8402 (pttm) REVERT: C 89 ASN cc_start: 0.7985 (p0) cc_final: 0.7707 (p0) REVERT: C 262 ILE cc_start: 0.8053 (mp) cc_final: 0.7840 (mm) REVERT: C 271 LYS cc_start: 0.7952 (mttt) cc_final: 0.7706 (mttm) REVERT: D 110 THR cc_start: 0.7138 (p) cc_final: 0.6879 (p) outliers start: 20 outliers final: 18 residues processed: 108 average time/residue: 0.1706 time to fit residues: 25.2762 Evaluate side-chains 111 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7017 Z= 0.288 Angle : 0.586 10.379 9447 Z= 0.304 Chirality : 0.042 0.134 1010 Planarity : 0.005 0.056 1221 Dihedral : 7.768 74.397 985 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.63 % Allowed : 16.04 % Favored : 80.33 % 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: -2.80 (0.28), residues: 839 helix: -0.97 (0.27), residues: 358 sheet: -2.51 (0.45), residues: 123 loop : -2.45 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 261 HIS 0.006 0.001 HIS B 202 PHE 0.011 0.001 PHE B 78 TYR 0.019 0.001 TYR A 37 ARG 0.003 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7119 (t80) REVERT: A 229 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8317 (pttt) REVERT: B 306 GLN cc_start: 0.6527 (pp30) cc_final: 0.6277 (pp30) REVERT: B 467 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8159 (m-70) REVERT: C 89 ASN cc_start: 0.7982 (p0) cc_final: 0.7627 (p0) REVERT: C 236 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7659 (mp) REVERT: C 262 ILE cc_start: 0.8085 (mp) cc_final: 0.7825 (mm) REVERT: C 271 LYS cc_start: 0.7987 (mttt) cc_final: 0.7725 (mttm) REVERT: D 110 THR cc_start: 0.7175 (p) cc_final: 0.6956 (p) REVERT: D 119 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8036 (mp0) outliers start: 26 outliers final: 18 residues processed: 113 average time/residue: 0.1747 time to fit residues: 27.2333 Evaluate side-chains 116 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.0670 chunk 76 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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: 0.7903 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7017 Z= 0.242 Angle : 0.577 12.187 9447 Z= 0.297 Chirality : 0.042 0.134 1010 Planarity : 0.004 0.055 1221 Dihedral : 7.711 77.096 985 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.93 % Allowed : 17.43 % Favored : 79.64 % 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: -2.70 (0.29), residues: 839 helix: -0.90 (0.27), residues: 360 sheet: -2.43 (0.46), residues: 123 loop : -2.41 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.010 0.001 PHE A 78 TYR 0.013 0.001 TYR A 37 ARG 0.003 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7245 (t80) REVERT: A 128 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7162 (t80) REVERT: A 229 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8356 (pttm) REVERT: B 467 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8164 (m-70) REVERT: C 89 ASN cc_start: 0.7803 (p0) cc_final: 0.7550 (p0) REVERT: C 236 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7618 (mp) REVERT: C 262 ILE cc_start: 0.8078 (mp) cc_final: 0.7838 (mm) REVERT: C 271 LYS cc_start: 0.8008 (mttt) cc_final: 0.7764 (mttm) REVERT: D 110 THR cc_start: 0.7166 (p) cc_final: 0.6950 (p) outliers start: 21 outliers final: 17 residues processed: 108 average time/residue: 0.1772 time to fit residues: 26.5486 Evaluate side-chains 111 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.0270 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.0060 chunk 53 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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: 0.7853 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7017 Z= 0.165 Angle : 0.560 12.292 9447 Z= 0.290 Chirality : 0.041 0.138 1010 Planarity : 0.004 0.057 1221 Dihedral : 7.450 76.023 985 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.07 % Allowed : 17.57 % Favored : 79.36 % 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: -2.47 (0.29), residues: 839 helix: -0.70 (0.28), residues: 360 sheet: -2.30 (0.47), residues: 123 loop : -2.32 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.018 0.001 PHE B 233 TYR 0.012 0.001 TYR D 138 ARG 0.002 0.000 ARG D 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7092 (t80) REVERT: A 128 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7131 (t80) REVERT: A 229 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8329 (pttm) REVERT: B 467 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.8224 (m-70) REVERT: C 89 ASN cc_start: 0.7778 (p0) cc_final: 0.7508 (p0) REVERT: C 262 ILE cc_start: 0.8081 (mp) cc_final: 0.7860 (mm) REVERT: C 271 LYS cc_start: 0.8015 (mttt) cc_final: 0.7793 (mttm) REVERT: D 110 THR cc_start: 0.7156 (p) cc_final: 0.6917 (p) outliers start: 22 outliers final: 18 residues processed: 106 average time/residue: 0.1817 time to fit residues: 26.5612 Evaluate side-chains 114 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110918 restraints weight = 12330.578| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.75 r_work: 0.3343 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7017 Z= 0.223 Angle : 0.572 12.878 9447 Z= 0.295 Chirality : 0.041 0.136 1010 Planarity : 0.004 0.055 1221 Dihedral : 7.624 80.246 985 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.49 % Allowed : 17.85 % Favored : 78.66 % 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: -2.53 (0.29), residues: 839 helix: -0.73 (0.28), residues: 358 sheet: -2.33 (0.46), residues: 123 loop : -2.35 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.017 0.001 PHE B 233 TYR 0.015 0.001 TYR A 37 ARG 0.002 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.83 seconds wall clock time: 33 minutes 9.66 seconds (1989.66 seconds total)