Starting phenix.real_space_refine on Wed Feb 14 02:55:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8w_31494/02_2024/7f8w_31494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8w_31494/02_2024/7f8w_31494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8w_31494/02_2024/7f8w_31494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8w_31494/02_2024/7f8w_31494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8w_31494/02_2024/7f8w_31494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8w_31494/02_2024/7f8w_31494_updated.pdb" } resolution = 3.1 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= 0.003 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5421 2.51 5 N 1449 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1850 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2347 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 300} Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "D" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 133 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2128 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 4.79, per 1000 atoms: 0.56 Number of scatterers: 8486 At special positions: 0 Unit cell: (128.535, 117.04, 90.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1556 8.00 N 1449 7.00 C 5421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 113 " distance=2.04 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 30.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.978A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.556A pdb=" N HIS A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 214 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'R' and resid 56 through 80 Processing helix chain 'R' and resid 88 through 116 Proline residue: R 109 - end of helix Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 124 through 156 Processing helix chain 'R' and resid 159 through 165 Processing helix chain 'R' and resid 168 through 185 Processing helix chain 'R' and resid 187 through 189 No H-bonds generated for 'chain 'R' and resid 187 through 189' Processing helix chain 'R' and resid 212 through 225 Processing helix chain 'R' and resid 228 through 248 Processing helix chain 'R' and resid 327 through 358 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 363 through 366 No H-bonds generated for 'chain 'R' and resid 363 through 366' Processing helix chain 'R' and resid 370 through 390 removed outlier: 3.787A pdb=" N SER R 379 " --> pdb=" O ILE R 375 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 395 through 404 Processing sheet with id= A, first strand: chain 'A' and resid 220 through 222 removed outlier: 5.976A pdb=" N LEU A 37 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 36 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.030A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.546A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.941A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.890A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.513A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.843A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 20 through 24 removed outlier: 3.552A pdb=" N GLN D 20 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 86 " --> pdb=" O GLN D 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'D' and resid 55 through 57 Processing sheet with id= L, first strand: chain 'D' and resid 163 through 165 removed outlier: 6.766A pdb=" N LYS D 261 " --> pdb=" O VAL D 164 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 172 through 176 Processing sheet with id= N, first strand: chain 'D' and resid 243 through 248 removed outlier: 3.756A pdb=" N TYR D 245 " --> pdb=" O PHE D 194 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1835 1.33 - 1.45: 2081 1.45 - 1.58: 4667 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 8674 Sorted by residual: bond pdb=" N MET D 247 " pdb=" CA MET D 247 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.26e-02 6.30e+03 8.86e+00 bond pdb=" N GLN D 248 " pdb=" CA GLN D 248 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.27e-02 6.20e+03 8.42e+00 bond pdb=" N CYS R 107 " pdb=" CA CYS R 107 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.06e+00 bond pdb=" N MET R 108 " pdb=" CA MET R 108 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.66e+00 bond pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.64e+00 ... (remaining 8669 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.32: 161 105.32 - 112.55: 4313 112.55 - 119.77: 3045 119.77 - 126.99: 4138 126.99 - 134.21: 114 Bond angle restraints: 11771 Sorted by residual: angle pdb=" C ARG D 208 " pdb=" N MET D 209 " pdb=" CA MET D 209 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N GLN D 248 " pdb=" CA GLN D 248 " pdb=" CB GLN D 248 " ideal model delta sigma weight residual 110.41 117.79 -7.38 1.63e+00 3.76e-01 2.05e+01 angle pdb=" CA ARG R 158 " pdb=" CB ARG R 158 " pdb=" CG ARG R 158 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" N PCA E 1 " pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 110.50 103.43 7.07 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CA LYS A 17 " pdb=" CB LYS A 17 " pdb=" CG LYS A 17 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.64e+01 ... (remaining 11766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4644 17.98 - 35.95: 390 35.95 - 53.93: 76 53.93 - 71.91: 7 71.91 - 89.89: 7 Dihedral angle restraints: 5124 sinusoidal: 1980 harmonic: 3144 Sorted by residual: dihedral pdb=" CA VAL R 164 " pdb=" C VAL R 164 " pdb=" N TRP R 165 " pdb=" CA TRP R 165 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU A 33 " pdb=" C GLU A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 66 " pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1021 0.062 - 0.125: 251 0.125 - 0.187: 59 0.187 - 0.249: 5 0.249 - 0.311: 3 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CB THR A 254 " pdb=" CA THR A 254 " pdb=" OG1 THR A 254 " pdb=" CG2 THR A 254 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ARG R 158 " pdb=" N ARG R 158 " pdb=" C ARG R 158 " pdb=" CB ARG R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1336 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA E 1 " 0.066 2.00e-02 2.50e+03 4.39e-02 2.41e+01 pdb=" CA PCA E 1 " -0.055 2.00e-02 2.50e+03 pdb=" CG PCA E 1 " 0.021 2.00e-02 2.50e+03 pdb=" CD PCA E 1 " 0.009 2.00e-02 2.50e+03 pdb=" OE PCA E 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " 0.027 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP B 332 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 245 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR D 245 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR D 245 " 0.024 2.00e-02 2.50e+03 pdb=" N CYS D 246 " 0.021 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2004 2.80 - 3.32: 7808 3.32 - 3.85: 14490 3.85 - 4.37: 16226 4.37 - 4.90: 28197 Nonbonded interactions: 68725 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.273 2.440 nonbonded pdb=" O VAL A 13 " pdb=" OG SER A 16 " model vdw 2.294 2.440 nonbonded pdb=" OG SER D 47 " pdb=" OD1 ASP D 91 " model vdw 2.301 2.440 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.307 2.440 nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.313 2.520 ... (remaining 68720 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: 0.870 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: 3.810 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.980 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 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 : 0.005 0.062 8674 Z= 0.331 Angle : 1.039 11.208 11771 Z= 0.554 Chirality : 0.059 0.311 1339 Planarity : 0.008 0.087 1484 Dihedral : 14.087 89.886 3094 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -1.99 (0.23), residues: 1067 helix: -0.31 (0.26), residues: 308 sheet: -1.21 (0.33), residues: 242 loop : -2.00 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP B 332 HIS 0.013 0.002 HIS A 212 PHE 0.041 0.003 PHE B 234 TYR 0.022 0.002 TYR A 279 ARG 0.014 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.013 Fit side-chains REVERT: A 26 ASP cc_start: 0.6145 (m-30) cc_final: 0.5893 (m-30) REVERT: A 242 MET cc_start: 0.4577 (tpt) cc_final: 0.4270 (tpt) REVERT: A 306 MET cc_start: 0.5356 (tmm) cc_final: 0.5114 (ttt) REVERT: B 111 TYR cc_start: 0.6260 (m-80) cc_final: 0.5894 (m-80) REVERT: D 115 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.6208 (ptt180) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2148 time to fit residues: 48.7891 Evaluate side-chains 120 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS R 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8674 Z= 0.241 Angle : 0.673 9.234 11771 Z= 0.345 Chirality : 0.044 0.178 1339 Planarity : 0.005 0.056 1484 Dihedral : 5.101 22.115 1189 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.63 % Allowed : 11.29 % Favored : 87.08 % 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: -1.34 (0.24), residues: 1067 helix: 0.73 (0.28), residues: 310 sheet: -1.19 (0.32), residues: 258 loop : -1.76 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 165 HIS 0.006 0.001 HIS B 142 PHE 0.019 0.002 PHE A 302 TYR 0.015 0.002 TYR A 319 ARG 0.004 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.936 Fit side-chains REVERT: A 26 ASP cc_start: 0.6067 (m-30) cc_final: 0.5781 (m-30) REVERT: A 242 MET cc_start: 0.4872 (tpt) cc_final: 0.4596 (tpt) REVERT: A 334 VAL cc_start: 0.6545 (m) cc_final: 0.6253 (m) REVERT: B 188 MET cc_start: 0.6886 (mmm) cc_final: 0.6488 (tpt) REVERT: B 234 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5080 (t80) REVERT: D 110 MET cc_start: 0.6553 (tpp) cc_final: 0.6214 (tpp) REVERT: R 65 PHE cc_start: 0.5409 (t80) cc_final: 0.5169 (t80) REVERT: R 186 MET cc_start: 0.1792 (tmm) cc_final: 0.1213 (ttt) outliers start: 15 outliers final: 10 residues processed: 135 average time/residue: 0.1874 time to fit residues: 35.8682 Evaluate side-chains 126 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 204 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8674 Z= 0.261 Angle : 0.652 9.249 11771 Z= 0.335 Chirality : 0.043 0.170 1339 Planarity : 0.005 0.047 1484 Dihedral : 5.041 24.142 1189 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.93 % Allowed : 14.44 % Favored : 82.63 % 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: -1.13 (0.25), residues: 1067 helix: 1.07 (0.28), residues: 317 sheet: -1.36 (0.30), residues: 276 loop : -1.60 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 165 HIS 0.005 0.001 HIS R 207 PHE 0.021 0.002 PHE B 234 TYR 0.016 0.002 TYR A 319 ARG 0.004 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.032 Fit side-chains REVERT: A 26 ASP cc_start: 0.6215 (m-30) cc_final: 0.5952 (m-30) REVERT: A 228 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6477 (mt-10) REVERT: B 234 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5175 (t80) REVERT: D 183 LEU cc_start: 0.5003 (OUTLIER) cc_final: 0.4228 (tt) REVERT: R 229 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6120 (mt) outliers start: 27 outliers final: 17 residues processed: 146 average time/residue: 0.1859 time to fit residues: 38.5993 Evaluate side-chains 138 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8674 Z= 0.306 Angle : 0.681 10.747 11771 Z= 0.350 Chirality : 0.044 0.176 1339 Planarity : 0.005 0.052 1484 Dihedral : 5.175 27.896 1189 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.13 % Allowed : 16.94 % Favored : 78.94 % 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: -1.20 (0.25), residues: 1067 helix: 1.06 (0.28), residues: 318 sheet: -1.56 (0.30), residues: 289 loop : -1.55 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 165 HIS 0.005 0.002 HIS B 62 PHE 0.022 0.002 PHE B 234 TYR 0.025 0.002 TYR R 380 ARG 0.005 0.001 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 0.803 Fit side-chains REVERT: A 26 ASP cc_start: 0.6273 (m-30) cc_final: 0.5965 (m-30) REVERT: B 99 TRP cc_start: 0.7326 (m100) cc_final: 0.7097 (m100) REVERT: B 118 ASP cc_start: 0.7619 (t0) cc_final: 0.7417 (t0) REVERT: B 234 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.5711 (t80) REVERT: B 284 LEU cc_start: 0.7602 (tt) cc_final: 0.7210 (tp) REVERT: C 50 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6497 (mm) REVERT: D 110 MET cc_start: 0.6488 (tpp) cc_final: 0.6005 (tpp) REVERT: R 229 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6176 (mt) outliers start: 38 outliers final: 23 residues processed: 157 average time/residue: 0.1912 time to fit residues: 42.5250 Evaluate side-chains 140 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 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 231 GLN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8674 Z= 0.229 Angle : 0.632 9.070 11771 Z= 0.322 Chirality : 0.042 0.164 1339 Planarity : 0.004 0.046 1484 Dihedral : 4.995 27.095 1189 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.67 % Allowed : 16.94 % Favored : 78.39 % 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: -1.09 (0.26), residues: 1067 helix: 1.24 (0.28), residues: 318 sheet: -1.53 (0.30), residues: 281 loop : -1.53 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 165 HIS 0.004 0.001 HIS C 44 PHE 0.017 0.002 PHE B 234 TYR 0.025 0.002 TYR R 380 ARG 0.005 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 0.983 Fit side-chains REVERT: A 26 ASP cc_start: 0.6126 (m-30) cc_final: 0.5886 (m-30) REVERT: B 42 ARG cc_start: 0.5696 (ttp80) cc_final: 0.5450 (tpt170) REVERT: B 234 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.5471 (t80) REVERT: B 284 LEU cc_start: 0.7544 (tt) cc_final: 0.7208 (tp) REVERT: C 50 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6212 (mm) REVERT: D 110 MET cc_start: 0.6512 (tpp) cc_final: 0.6071 (tpp) REVERT: R 229 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6159 (mt) outliers start: 43 outliers final: 23 residues processed: 153 average time/residue: 0.1856 time to fit residues: 40.3050 Evaluate side-chains 138 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8674 Z= 0.189 Angle : 0.613 10.519 11771 Z= 0.311 Chirality : 0.042 0.161 1339 Planarity : 0.004 0.042 1484 Dihedral : 4.750 26.384 1189 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.47 % Allowed : 18.35 % Favored : 78.18 % 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: -0.92 (0.26), residues: 1067 helix: 1.46 (0.28), residues: 317 sheet: -1.49 (0.30), residues: 281 loop : -1.45 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS C 44 PHE 0.015 0.002 PHE B 292 TYR 0.015 0.001 TYR A 319 ARG 0.006 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 0.953 Fit side-chains REVERT: A 26 ASP cc_start: 0.6022 (m-30) cc_final: 0.5792 (m-30) REVERT: C 50 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6499 (mt) REVERT: D 110 MET cc_start: 0.6447 (tpp) cc_final: 0.6038 (tpp) REVERT: R 134 MET cc_start: 0.5561 (mmp) cc_final: 0.5296 (mmp) REVERT: R 229 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6127 (mt) outliers start: 32 outliers final: 23 residues processed: 145 average time/residue: 0.1893 time to fit residues: 38.8636 Evaluate side-chains 141 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8674 Z= 0.292 Angle : 0.681 10.651 11771 Z= 0.347 Chirality : 0.044 0.179 1339 Planarity : 0.004 0.047 1484 Dihedral : 5.026 25.905 1189 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.13 % Allowed : 18.89 % Favored : 76.98 % 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: -0.96 (0.26), residues: 1067 helix: 1.32 (0.28), residues: 318 sheet: -1.48 (0.30), residues: 288 loop : -1.41 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 346 HIS 0.005 0.001 HIS B 62 PHE 0.019 0.002 PHE B 234 TYR 0.020 0.002 TYR R 380 ARG 0.007 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 115 time to evaluate : 0.958 Fit side-chains REVERT: A 26 ASP cc_start: 0.6147 (m-30) cc_final: 0.5869 (m-30) REVERT: B 81 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6863 (mm) REVERT: B 234 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.5677 (t80) REVERT: R 229 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6091 (mt) outliers start: 38 outliers final: 27 residues processed: 142 average time/residue: 0.1876 time to fit residues: 37.5397 Evaluate side-chains 139 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8674 Z= 0.253 Angle : 0.679 12.834 11771 Z= 0.342 Chirality : 0.044 0.173 1339 Planarity : 0.004 0.046 1484 Dihedral : 4.959 25.336 1189 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.91 % Allowed : 20.30 % Favored : 75.79 % 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: -0.97 (0.26), residues: 1067 helix: 1.27 (0.28), residues: 319 sheet: -1.48 (0.30), residues: 289 loop : -1.38 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.019 0.002 PHE B 234 TYR 0.019 0.002 TYR A 319 ARG 0.007 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 0.900 Fit side-chains REVERT: A 26 ASP cc_start: 0.6371 (m-30) cc_final: 0.6069 (m-30) REVERT: B 81 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6864 (mm) REVERT: B 234 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.5635 (t80) REVERT: D 110 MET cc_start: 0.6537 (tpp) cc_final: 0.5999 (tpp) REVERT: R 134 MET cc_start: 0.5659 (mmp) cc_final: 0.5362 (mmp) REVERT: R 229 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.6130 (mp) outliers start: 36 outliers final: 29 residues processed: 144 average time/residue: 0.1869 time to fit residues: 38.0996 Evaluate side-chains 145 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8674 Z= 0.224 Angle : 0.675 13.712 11771 Z= 0.338 Chirality : 0.043 0.176 1339 Planarity : 0.004 0.043 1484 Dihedral : 4.901 24.593 1189 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.69 % Allowed : 20.74 % Favored : 75.57 % 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: -0.95 (0.26), residues: 1067 helix: 1.31 (0.28), residues: 318 sheet: -1.48 (0.30), residues: 289 loop : -1.37 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.032 0.002 PHE R 120 TYR 0.017 0.002 TYR A 319 ARG 0.007 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.055 Fit side-chains REVERT: A 26 ASP cc_start: 0.6348 (m-30) cc_final: 0.6030 (m-30) REVERT: B 81 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6829 (mm) REVERT: B 234 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.5605 (t80) REVERT: D 110 MET cc_start: 0.6438 (tpp) cc_final: 0.6011 (tpp) REVERT: D 183 LEU cc_start: 0.5457 (OUTLIER) cc_final: 0.5246 (tt) REVERT: R 229 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6002 (tp) outliers start: 34 outliers final: 30 residues processed: 142 average time/residue: 0.1947 time to fit residues: 39.1555 Evaluate side-chains 149 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 HIS Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 0.0050 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.0000 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8674 Z= 0.194 Angle : 0.658 12.897 11771 Z= 0.329 Chirality : 0.043 0.170 1339 Planarity : 0.004 0.042 1484 Dihedral : 4.741 23.141 1189 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.58 % Allowed : 21.06 % Favored : 75.35 % 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: -0.85 (0.26), residues: 1067 helix: 1.40 (0.28), residues: 318 sheet: -1.43 (0.30), residues: 289 loop : -1.32 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.006 0.001 HIS C 44 PHE 0.024 0.002 PHE R 120 TYR 0.014 0.001 TYR A 319 ARG 0.007 0.000 ARG D 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 0.973 Fit side-chains REVERT: A 26 ASP cc_start: 0.6288 (m-30) cc_final: 0.5974 (m-30) REVERT: B 81 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6917 (mm) REVERT: B 234 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.5540 (t80) REVERT: D 110 MET cc_start: 0.6365 (tpp) cc_final: 0.5895 (tpp) REVERT: R 186 MET cc_start: 0.3522 (tmm) cc_final: 0.2873 (tpp) REVERT: R 229 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.6164 (tt) outliers start: 33 outliers final: 26 residues processed: 143 average time/residue: 0.1848 time to fit residues: 37.8398 Evaluate side-chains 144 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.207786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.169852 restraints weight = 10634.997| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.46 r_work: 0.4262 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8674 Z= 0.182 Angle : 0.662 12.330 11771 Z= 0.327 Chirality : 0.043 0.183 1339 Planarity : 0.004 0.037 1484 Dihedral : 4.661 25.946 1189 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.47 % Allowed : 22.04 % Favored : 74.48 % 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: -0.77 (0.26), residues: 1067 helix: 1.43 (0.28), residues: 321 sheet: -1.39 (0.30), residues: 283 loop : -1.27 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.007 0.001 HIS C 44 PHE 0.022 0.002 PHE R 120 TYR 0.013 0.001 TYR A 319 ARG 0.007 0.000 ARG D 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.26 seconds wall clock time: 40 minutes 18.66 seconds (2418.66 seconds total)