Starting phenix.real_space_refine on Mon Mar 11 04:16:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/03_2024/7l0r_23101.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/03_2024/7l0r_23101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/03_2024/7l0r_23101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/03_2024/7l0r_23101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/03_2024/7l0r_23101.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0r_23101/03_2024/7l0r_23101.pdb" } resolution = 4.2 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= 0.002 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 53 5.16 5 C 4450 2.51 5 N 1176 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 8": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6968 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2424 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2385 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Chain: "G" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 310 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Time building chain proxies: 4.16, per 1000 atoms: 0.60 Number of scatterers: 6968 At special positions: 0 Unit cell: (75.075, 112.2, 121.275, 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 53 16.00 O 1289 8.00 N 1176 7.00 C 4450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 225 " 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: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 43.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'C' and resid 60 through 91 Processing helix chain 'C' and resid 100 through 129 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 137 through 173 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 182 through 202 Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.519A pdb=" N THR C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 270 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 300 through 334 Proline residue: C 323 - end of helix removed outlier: 3.533A pdb=" N ILE C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 371 Proline residue: C 366 - end of helix Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.508A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.781A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.405A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'G' and resid 32 through 48 Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.527A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.895A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.837A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.974A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.399A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.063A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.903A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1062 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: 2.10 Time building geometry restraints manager: 2.89 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: 1875 1.33 - 1.45: 1457 1.45 - 1.57: 3699 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 7108 Sorted by residual: bond pdb=" C HIS C 133 " pdb=" N PRO C 134 " ideal model delta sigma weight residual 1.331 1.385 -0.053 1.28e-02 6.10e+03 1.72e+01 bond pdb=" N LEU B 95 " pdb=" CA LEU B 95 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.30e+00 bond pdb=" N ASP A 309 " pdb=" CA ASP A 309 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.33e-02 5.65e+03 6.36e+00 bond pdb=" N LEU C 256 " pdb=" CA LEU C 256 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.14e+00 bond pdb=" N ASP B 323 " pdb=" CA ASP B 323 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.83e+00 ... (remaining 7103 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.03: 131 106.03 - 113.06: 3725 113.06 - 120.09: 2857 120.09 - 127.12: 2830 127.12 - 134.15: 88 Bond angle restraints: 9631 Sorted by residual: angle pdb=" N PHE C 376 " pdb=" CA PHE C 376 " pdb=" C PHE C 376 " ideal model delta sigma weight residual 112.54 105.52 7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N VAL C 131 " pdb=" CA VAL C 131 " pdb=" C VAL C 131 " ideal model delta sigma weight residual 107.51 99.00 8.51 1.49e+00 4.50e-01 3.26e+01 angle pdb=" N LYS A 46 " pdb=" CA LYS A 46 " pdb=" C LYS A 46 " ideal model delta sigma weight residual 111.28 105.13 6.15 1.09e+00 8.42e-01 3.18e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.82 127.90 -7.08 1.47e+00 4.63e-01 2.32e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 ... (remaining 9626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 3770 15.98 - 31.96: 329 31.96 - 47.93: 77 47.93 - 63.91: 24 63.91 - 79.89: 4 Dihedral angle restraints: 4204 sinusoidal: 1628 harmonic: 2576 Sorted by residual: dihedral pdb=" CB CYS C 142 " pdb=" SG CYS C 142 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -165.89 79.89 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CA PHE G 64 " pdb=" C PHE G 64 " pdb=" N LYS G 65 " pdb=" CA LYS G 65 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 4201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 836 0.082 - 0.164: 221 0.164 - 0.246: 41 0.246 - 0.328: 13 0.328 - 0.410: 1 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA HIS C 133 " pdb=" N HIS C 133 " pdb=" C HIS C 133 " pdb=" CB HIS C 133 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+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 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB VAL C 266 " pdb=" CA VAL C 266 " pdb=" CG1 VAL C 266 " pdb=" CG2 VAL C 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1109 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 374 " 0.027 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C ALA C 374 " -0.092 2.00e-02 2.50e+03 pdb=" O ALA C 374 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN C 375 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 49 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG B 49 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG B 49 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 50 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 300 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.01e+01 pdb=" C VAL C 300 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL C 300 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 301 " -0.018 2.00e-02 2.50e+03 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 201 2.66 - 3.22: 6562 3.22 - 3.78: 11590 3.78 - 4.34: 14908 4.34 - 4.90: 24418 Nonbonded interactions: 57679 Sorted by model distance: nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.106 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.232 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 2.440 nonbonded pdb=" N GLU A 43 " pdb=" OE1 GLU A 43 " model vdw 2.286 2.520 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.304 2.440 ... (remaining 57674 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.450 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 0.081 7108 Z= 0.479 Angle : 1.372 10.325 9631 Z= 0.787 Chirality : 0.079 0.410 1112 Planarity : 0.008 0.058 1209 Dihedral : 13.578 70.468 2535 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.05 % Allowed : 11.26 % Favored : 87.70 % Cbeta Deviations : 0.24 % 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: -3.44 (0.24), residues: 869 helix: -1.98 (0.20), residues: 376 sheet: -2.25 (0.36), residues: 173 loop : -2.41 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP B 297 HIS 0.008 0.003 HIS A 188 PHE 0.038 0.004 PHE C 376 TYR 0.029 0.004 TYR C 349 ARG 0.012 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 301 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 LEU cc_start: 0.8671 (tp) cc_final: 0.8437 (tp) REVERT: C 305 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8325 (mtt-85) REVERT: A 21 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7589 (tpp80) REVERT: A 22 ASN cc_start: 0.8967 (m-40) cc_final: 0.8759 (m110) REVERT: A 28 GLU cc_start: 0.8303 (tt0) cc_final: 0.7854 (tm-30) REVERT: A 321 THR cc_start: 0.7498 (p) cc_final: 0.7253 (p) REVERT: B 46 ARG cc_start: 0.6912 (tpt-90) cc_final: 0.6697 (mtp-110) REVERT: B 51 LEU cc_start: 0.8445 (mp) cc_final: 0.8086 (mp) REVERT: B 79 LEU cc_start: 0.9142 (pt) cc_final: 0.8914 (pp) REVERT: B 82 TRP cc_start: 0.8585 (m100) cc_final: 0.8375 (m100) REVERT: B 93 ILE cc_start: 0.9144 (mt) cc_final: 0.8895 (mt) REVERT: B 99 TRP cc_start: 0.8466 (m100) cc_final: 0.8052 (m100) REVERT: B 126 LEU cc_start: 0.8266 (mp) cc_final: 0.8017 (mp) REVERT: B 149 CYS cc_start: 0.8130 (p) cc_final: 0.7716 (m) REVERT: B 188 MET cc_start: 0.8407 (mmm) cc_final: 0.8064 (mmm) REVERT: B 308 LEU cc_start: 0.8750 (tp) cc_final: 0.7640 (tp) REVERT: B 312 ASP cc_start: 0.7384 (p0) cc_final: 0.6928 (t0) REVERT: B 329 THR cc_start: 0.9075 (t) cc_final: 0.8805 (t) outliers start: 8 outliers final: 3 residues processed: 306 average time/residue: 0.2368 time to fit residues: 90.2364 Evaluate side-chains 206 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 159 ASN C 219 HIS C 239 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7108 Z= 0.195 Angle : 0.686 7.832 9631 Z= 0.364 Chirality : 0.045 0.183 1112 Planarity : 0.005 0.040 1209 Dihedral : 5.411 28.134 955 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % 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: -1.97 (0.25), residues: 869 helix: -0.32 (0.24), residues: 381 sheet: -1.41 (0.35), residues: 176 loop : -2.37 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 339 HIS 0.011 0.002 HIS C 325 PHE 0.042 0.002 PHE C 246 TYR 0.018 0.002 TYR C 369 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 LEU cc_start: 0.8189 (tp) cc_final: 0.7893 (tp) REVERT: C 345 ASP cc_start: 0.8560 (m-30) cc_final: 0.8048 (m-30) REVERT: C 357 LEU cc_start: 0.8920 (mt) cc_final: 0.8711 (mt) REVERT: A 18 MET cc_start: 0.8566 (tpp) cc_final: 0.8213 (tpp) REVERT: A 28 GLU cc_start: 0.8377 (tt0) cc_final: 0.8036 (tm-30) REVERT: B 59 TYR cc_start: 0.8660 (m-80) cc_final: 0.8257 (m-80) REVERT: B 61 MET cc_start: 0.7683 (ppp) cc_final: 0.7427 (ppp) REVERT: B 212 ASP cc_start: 0.5355 (t0) cc_final: 0.4672 (t0) REVERT: B 312 ASP cc_start: 0.7548 (p0) cc_final: 0.6752 (t70) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.2065 time to fit residues: 72.1571 Evaluate side-chains 186 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 HIS C 159 ASN C 239 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN A 306 GLN B 88 ASN B 142 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7108 Z= 0.198 Angle : 0.659 7.620 9631 Z= 0.348 Chirality : 0.044 0.184 1112 Planarity : 0.004 0.046 1209 Dihedral : 4.988 17.870 955 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.81 % 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 (0.27), residues: 869 helix: 0.36 (0.25), residues: 379 sheet: -1.22 (0.36), residues: 180 loop : -2.19 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.008 0.001 HIS B 311 PHE 0.024 0.002 PHE C 344 TYR 0.016 0.002 TYR B 85 ARG 0.010 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 345 ASP cc_start: 0.8566 (m-30) cc_final: 0.8030 (m-30) REVERT: C 357 LEU cc_start: 0.8952 (mt) cc_final: 0.8748 (mt) REVERT: A 28 GLU cc_start: 0.8256 (tt0) cc_final: 0.8016 (tm-30) REVERT: A 196 PHE cc_start: 0.7944 (m-80) cc_final: 0.7720 (m-80) REVERT: A 204 GLN cc_start: 0.7342 (pp30) cc_final: 0.6943 (pp30) REVERT: B 61 MET cc_start: 0.7592 (ppp) cc_final: 0.7316 (ppp) REVERT: B 82 TRP cc_start: 0.7529 (m-10) cc_final: 0.7192 (m-10) REVERT: G 41 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7576 (tmt170) outliers start: 1 outliers final: 1 residues processed: 242 average time/residue: 0.2088 time to fit residues: 65.1634 Evaluate side-chains 185 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS A 52 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7108 Z= 0.224 Angle : 0.644 7.128 9631 Z= 0.342 Chirality : 0.044 0.157 1112 Planarity : 0.004 0.046 1209 Dihedral : 4.943 18.754 955 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % 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: -0.83 (0.28), residues: 869 helix: 0.82 (0.26), residues: 377 sheet: -0.99 (0.36), residues: 185 loop : -1.94 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 135 HIS 0.009 0.001 HIS B 311 PHE 0.027 0.002 PHE C 344 TYR 0.017 0.002 TYR C 349 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 LEU cc_start: 0.7359 (tt) cc_final: 0.7157 (tp) REVERT: C 305 ARG cc_start: 0.8846 (mtt90) cc_final: 0.8458 (mtt-85) REVERT: C 345 ASP cc_start: 0.8627 (m-30) cc_final: 0.8166 (m-30) REVERT: A 209 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8187 (ttpp) REVERT: B 61 MET cc_start: 0.7596 (ppp) cc_final: 0.7363 (ppp) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2102 time to fit residues: 64.9426 Evaluate side-chains 175 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN B 142 HIS B 230 ASN B 295 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7108 Z= 0.203 Angle : 0.656 7.963 9631 Z= 0.346 Chirality : 0.044 0.184 1112 Planarity : 0.004 0.047 1209 Dihedral : 4.866 17.496 955 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.13 % Allowed : 2.49 % Favored : 97.38 % 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: -0.58 (0.28), residues: 869 helix: 0.92 (0.26), residues: 377 sheet: -0.60 (0.37), residues: 187 loop : -1.87 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.008 0.001 HIS B 311 PHE 0.027 0.002 PHE C 246 TYR 0.020 0.002 TYR C 324 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 MET cc_start: 0.7204 (ptp) cc_final: 0.6986 (ptp) REVERT: C 305 ARG cc_start: 0.8853 (mtt90) cc_final: 0.8435 (mtt-85) REVERT: C 345 ASP cc_start: 0.8631 (m-30) cc_final: 0.8084 (m-30) REVERT: C 346 PHE cc_start: 0.7638 (t80) cc_final: 0.7391 (t80) REVERT: A 195 HIS cc_start: 0.7272 (p90) cc_final: 0.6981 (p-80) REVERT: A 197 LYS cc_start: 0.8268 (mptt) cc_final: 0.7974 (mmtt) REVERT: A 209 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8119 (ttpp) REVERT: A 333 GLN cc_start: 0.7431 (pm20) cc_final: 0.7229 (pm20) REVERT: A 343 ILE cc_start: 0.9240 (tp) cc_final: 0.8952 (tp) REVERT: A 347 ASN cc_start: 0.8232 (m110) cc_final: 0.7847 (m110) REVERT: B 45 MET cc_start: 0.7241 (mmp) cc_final: 0.6753 (mmt) REVERT: B 59 TYR cc_start: 0.8533 (m-10) cc_final: 0.8213 (m-80) REVERT: B 61 MET cc_start: 0.7643 (ppp) cc_final: 0.7383 (ppp) REVERT: B 129 ARG cc_start: 0.8427 (ppt170) cc_final: 0.8203 (ttp80) REVERT: B 311 HIS cc_start: 0.6099 (m90) cc_final: 0.5879 (m-70) REVERT: B 331 SER cc_start: 0.8805 (p) cc_final: 0.8441 (t) REVERT: G 43 TYR cc_start: 0.8227 (t80) cc_final: 0.7972 (t80) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2191 time to fit residues: 65.6042 Evaluate side-chains 179 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7108 Z= 0.182 Angle : 0.647 7.997 9631 Z= 0.339 Chirality : 0.044 0.190 1112 Planarity : 0.004 0.050 1209 Dihedral : 4.780 16.908 955 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.39 % Allowed : 2.75 % Favored : 96.86 % 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: -0.35 (0.28), residues: 869 helix: 1.10 (0.26), residues: 375 sheet: -0.46 (0.38), residues: 181 loop : -1.72 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 297 HIS 0.012 0.001 HIS C 325 PHE 0.033 0.002 PHE C 246 TYR 0.020 0.002 TYR C 349 ARG 0.011 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 227 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 VAL cc_start: 0.8529 (t) cc_final: 0.7986 (p) REVERT: C 250 MET cc_start: 0.7199 (ptp) cc_final: 0.6992 (ptp) REVERT: C 305 ARG cc_start: 0.8837 (mtt90) cc_final: 0.8415 (mtt-85) REVERT: C 345 ASP cc_start: 0.8548 (m-30) cc_final: 0.8031 (m-30) REVERT: C 346 PHE cc_start: 0.7605 (t80) cc_final: 0.7305 (t80) REVERT: C 369 TYR cc_start: 0.4832 (m-80) cc_final: 0.4229 (m-80) REVERT: A 22 ASN cc_start: 0.8852 (m110) cc_final: 0.8650 (m110) REVERT: A 206 SER cc_start: 0.7294 (p) cc_final: 0.7084 (p) REVERT: A 209 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8025 (ttpp) REVERT: B 45 MET cc_start: 0.7320 (mmp) cc_final: 0.6781 (mmt) REVERT: B 59 TYR cc_start: 0.8489 (m-10) cc_final: 0.8038 (m-80) REVERT: B 61 MET cc_start: 0.7651 (ppp) cc_final: 0.7411 (ppp) REVERT: B 85 TYR cc_start: 0.7397 (m-80) cc_final: 0.7158 (m-80) REVERT: B 311 HIS cc_start: 0.6231 (m90) cc_final: 0.5844 (m-70) REVERT: B 331 SER cc_start: 0.8890 (p) cc_final: 0.8503 (t) REVERT: G 41 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8072 (ttp80) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.2097 time to fit residues: 61.4392 Evaluate side-chains 181 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 0.0070 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7108 Z= 0.188 Angle : 0.666 8.334 9631 Z= 0.345 Chirality : 0.044 0.185 1112 Planarity : 0.004 0.051 1209 Dihedral : 4.755 17.174 955 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.27 (0.29), residues: 869 helix: 1.05 (0.26), residues: 376 sheet: -0.21 (0.38), residues: 179 loop : -1.65 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.005 0.001 HIS B 225 PHE 0.024 0.001 PHE C 344 TYR 0.016 0.001 TYR C 146 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.8899 (mtt90) cc_final: 0.8421 (mtt-85) REVERT: C 345 ASP cc_start: 0.8557 (m-30) cc_final: 0.8157 (p0) REVERT: A 22 ASN cc_start: 0.8824 (m110) cc_final: 0.8596 (m110) REVERT: A 28 GLU cc_start: 0.8123 (tt0) cc_final: 0.7906 (tm-30) REVERT: A 206 SER cc_start: 0.7304 (p) cc_final: 0.7073 (p) REVERT: A 209 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8037 (ttpp) REVERT: A 316 THR cc_start: 0.8376 (p) cc_final: 0.8140 (p) REVERT: B 45 MET cc_start: 0.7357 (mmp) cc_final: 0.6755 (tpp) REVERT: B 59 TYR cc_start: 0.8487 (m-10) cc_final: 0.7971 (m-80) REVERT: B 61 MET cc_start: 0.7684 (ppp) cc_final: 0.7256 (ppp) REVERT: B 63 TRP cc_start: 0.7318 (m100) cc_final: 0.6911 (m100) REVERT: B 85 TYR cc_start: 0.7548 (m-80) cc_final: 0.7190 (m-80) REVERT: B 325 MET cc_start: 0.8404 (mmm) cc_final: 0.8121 (mmm) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2242 time to fit residues: 65.2495 Evaluate side-chains 177 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 0.0570 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7108 Z= 0.214 Angle : 0.695 10.129 9631 Z= 0.363 Chirality : 0.045 0.169 1112 Planarity : 0.005 0.056 1209 Dihedral : 4.835 17.890 955 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.19 (0.29), residues: 869 helix: 1.07 (0.26), residues: 375 sheet: -0.09 (0.39), residues: 179 loop : -1.60 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 321 HIS 0.009 0.001 HIS B 311 PHE 0.025 0.002 PHE C 344 TYR 0.018 0.002 TYR C 146 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 VAL cc_start: 0.8551 (t) cc_final: 0.7935 (p) REVERT: C 190 ILE cc_start: 0.7753 (pt) cc_final: 0.7548 (pt) REVERT: C 250 MET cc_start: 0.7148 (ptp) cc_final: 0.6889 (ptp) REVERT: C 305 ARG cc_start: 0.8955 (mtt90) cc_final: 0.8467 (mtt-85) REVERT: C 345 ASP cc_start: 0.8592 (m-30) cc_final: 0.8075 (p0) REVERT: D 12 ILE cc_start: 0.7636 (mm) cc_final: 0.7366 (mm) REVERT: A 22 ASN cc_start: 0.8823 (m110) cc_final: 0.8577 (m110) REVERT: A 206 SER cc_start: 0.7299 (p) cc_final: 0.7071 (p) REVERT: A 209 LYS cc_start: 0.8393 (mtmt) cc_final: 0.7936 (ttpp) REVERT: B 85 TYR cc_start: 0.7630 (m-80) cc_final: 0.7249 (m-80) REVERT: B 129 ARG cc_start: 0.8486 (ppt170) cc_final: 0.8244 (ttp80) REVERT: G 31 MET cc_start: 0.3973 (mtt) cc_final: 0.3760 (mtp) REVERT: G 38 GLU cc_start: 0.8781 (tp30) cc_final: 0.7864 (tp30) REVERT: G 41 ARG cc_start: 0.8662 (ttp80) cc_final: 0.7919 (ttp80) REVERT: G 42 ASP cc_start: 0.9018 (p0) cc_final: 0.8161 (p0) REVERT: G 44 VAL cc_start: 0.7973 (p) cc_final: 0.7481 (p) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2036 time to fit residues: 58.1820 Evaluate side-chains 178 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 311 ASN B 175 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7108 Z= 0.265 Angle : 0.732 9.627 9631 Z= 0.380 Chirality : 0.046 0.178 1112 Planarity : 0.005 0.058 1209 Dihedral : 5.076 19.686 955 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.26 % Allowed : 0.65 % Favored : 99.08 % 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: -0.30 (0.28), residues: 869 helix: 1.02 (0.26), residues: 376 sheet: -0.32 (0.38), residues: 185 loop : -1.62 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.013 0.002 HIS B 311 PHE 0.025 0.002 PHE C 344 TYR 0.029 0.002 TYR B 59 ARG 0.013 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 VAL cc_start: 0.8584 (t) cc_final: 0.8058 (p) REVERT: C 190 ILE cc_start: 0.7738 (pt) cc_final: 0.7513 (pt) REVERT: C 345 ASP cc_start: 0.8531 (m-30) cc_final: 0.8210 (p0) REVERT: C 346 PHE cc_start: 0.7615 (t80) cc_final: 0.7396 (t80) REVERT: D 12 ILE cc_start: 0.7792 (mm) cc_final: 0.7418 (mm) REVERT: A 22 ASN cc_start: 0.8841 (m110) cc_final: 0.8619 (m110) REVERT: A 206 SER cc_start: 0.7714 (p) cc_final: 0.7422 (p) REVERT: A 209 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8004 (ttpp) REVERT: B 85 TYR cc_start: 0.7964 (m-80) cc_final: 0.7463 (m-10) REVERT: B 129 ARG cc_start: 0.8503 (ppt170) cc_final: 0.8288 (ttp80) REVERT: G 38 GLU cc_start: 0.8786 (tp30) cc_final: 0.8510 (tp30) REVERT: G 41 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8201 (tmt-80) REVERT: G 44 VAL cc_start: 0.7440 (p) cc_final: 0.7230 (p) outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.1934 time to fit residues: 54.0435 Evaluate side-chains 171 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7108 Z= 0.188 Angle : 0.695 9.268 9631 Z= 0.356 Chirality : 0.046 0.189 1112 Planarity : 0.005 0.064 1209 Dihedral : 4.960 17.490 955 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.20 (0.29), residues: 869 helix: 1.05 (0.26), residues: 376 sheet: -0.19 (0.39), residues: 181 loop : -1.54 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 339 HIS 0.008 0.001 HIS C 325 PHE 0.021 0.002 PHE C 344 TYR 0.020 0.002 TYR C 105 ARG 0.014 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 VAL cc_start: 0.8501 (t) cc_final: 0.7906 (p) REVERT: C 190 ILE cc_start: 0.7700 (pt) cc_final: 0.7451 (pt) REVERT: C 305 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8587 (mtp85) REVERT: C 345 ASP cc_start: 0.8492 (m-30) cc_final: 0.8105 (p0) REVERT: C 346 PHE cc_start: 0.7543 (t80) cc_final: 0.7311 (t80) REVERT: D 13 LEU cc_start: 0.5584 (tp) cc_final: 0.5338 (tt) REVERT: A 22 ASN cc_start: 0.8866 (m110) cc_final: 0.8642 (m110) REVERT: A 201 VAL cc_start: 0.8783 (t) cc_final: 0.8459 (p) REVERT: A 206 SER cc_start: 0.7338 (p) cc_final: 0.7072 (p) REVERT: A 209 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7896 (ttpp) REVERT: B 45 MET cc_start: 0.7318 (mmp) cc_final: 0.7017 (tpp) REVERT: B 63 TRP cc_start: 0.7347 (m100) cc_final: 0.7009 (m100) REVERT: B 85 TYR cc_start: 0.7657 (m-80) cc_final: 0.7254 (m-80) REVERT: B 123 ILE cc_start: 0.9024 (mm) cc_final: 0.8442 (pt) REVERT: B 129 ARG cc_start: 0.8506 (ppt170) cc_final: 0.8288 (ttp80) REVERT: G 38 GLU cc_start: 0.8667 (tp30) cc_final: 0.8406 (tp30) REVERT: G 41 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8145 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2157 time to fit residues: 60.6997 Evaluate side-chains 171 residues out of total 765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN A 304 GLN ** A 331 ASN ** 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 = 0.3862 r_free = 0.3862 target = 0.111529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090113 restraints weight = 21254.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092865 restraints weight = 12636.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094679 restraints weight = 8739.554| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7108 Z= 0.207 Angle : 0.701 8.881 9631 Z= 0.362 Chirality : 0.046 0.189 1112 Planarity : 0.005 0.058 1209 Dihedral : 4.914 20.711 955 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.16 (0.28), residues: 869 helix: 1.06 (0.26), residues: 375 sheet: -0.17 (0.38), residues: 181 loop : -1.46 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.012 0.001 HIS C 325 PHE 0.021 0.002 PHE C 344 TYR 0.014 0.002 TYR C 333 ARG 0.014 0.001 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.60 seconds wall clock time: 35 minutes 43.75 seconds (2143.75 seconds total)