Starting phenix.real_space_refine on Tue Mar 11 23:57:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l0r_23101/03_2025/7l0r_23101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l0r_23101/03_2025/7l0r_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/cci-nas-00/data/ceres_data/7l0r_23101/03_2025/7l0r_23101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l0r_23101/03_2025/7l0r_23101.map" model { file = "/net/cci-nas-00/data/ceres_data/7l0r_23101/03_2025/7l0r_23101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l0r_23101/03_2025/7l0r_23101.cif" } 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. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.50, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 980.9 milliseconds 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: 0.68 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: 1.99 Time building geometry restraints manager: 1.78 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: 0.00 - 2.06: 8677 2.06 - 4.13: 764 4.13 - 6.19: 132 6.19 - 8.26: 38 8.26 - 10.32: 20 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 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 3.040 nonbonded pdb=" N GLU A 43 " pdb=" OE1 GLU A 43 " model vdw 2.286 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.304 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.060 Find NCS groups from input model: 0.090 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 8 poor density : 301 time to evaluate : 0.762 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: 0.2303 time to fit residues: 88.0278 Evaluate side-chains 206 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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: 0.8980 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 292 ASN A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 295 ASN B 311 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.112370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091626 restraints weight = 21102.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094157 restraints weight = 13057.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095946 restraints weight = 9258.910| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7108 Z= 0.190 Angle : 0.707 8.937 9631 Z= 0.374 Chirality : 0.046 0.217 1112 Planarity : 0.005 0.040 1209 Dihedral : 5.739 59.180 955 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.25), residues: 869 helix: -0.38 (0.23), residues: 380 sheet: -1.45 (0.36), residues: 174 loop : -2.42 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 339 HIS 0.011 0.002 HIS C 325 PHE 0.043 0.002 PHE C 246 TYR 0.021 0.002 TYR C 369 ARG 0.008 0.001 ARG B 42 *********************** 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 273 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.744 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 167 ARG cc_start: 0.8401 (mtt-85) cc_final: 0.8174 (mtp85) REVERT: C 169 LEU cc_start: 0.8933 (tp) cc_final: 0.8714 (tp) REVERT: C 234 LEU cc_start: 0.9203 (tt) cc_final: 0.8852 (mt) REVERT: C 345 ASP cc_start: 0.8385 (m-30) cc_final: 0.7814 (m-30) REVERT: C 346 PHE cc_start: 0.8799 (t80) cc_final: 0.8452 (t80) REVERT: C 357 LEU cc_start: 0.9367 (mt) cc_final: 0.9072 (mt) REVERT: A 28 GLU cc_start: 0.8146 (tt0) cc_final: 0.7895 (tm-30) REVERT: A 204 GLN cc_start: 0.7788 (pp30) cc_final: 0.7430 (pp30) REVERT: A 243 MET cc_start: 0.8336 (tpp) cc_final: 0.7868 (tpp) REVERT: A 343 ILE cc_start: 0.9251 (tp) cc_final: 0.9022 (tp) REVERT: B 59 TYR cc_start: 0.8393 (m-80) cc_final: 0.7920 (m-80) REVERT: B 61 MET cc_start: 0.7834 (ppp) cc_final: 0.7552 (ppp) REVERT: B 149 CYS cc_start: 0.8086 (p) cc_final: 0.7725 (m) REVERT: B 212 ASP cc_start: 0.5669 (t0) cc_final: 0.4701 (t0) REVERT: B 261 LEU cc_start: 0.8818 (tt) cc_final: 0.8524 (tt) REVERT: B 325 MET cc_start: 0.8537 (mmm) cc_final: 0.8336 (mmm) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2050 time to fit residues: 72.9773 Evaluate side-chains 196 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 C 355 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 230 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.108689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088095 restraints weight = 22031.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090587 restraints weight = 13477.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092189 restraints weight = 9562.606| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7108 Z= 0.255 Angle : 0.703 7.522 9631 Z= 0.375 Chirality : 0.046 0.189 1112 Planarity : 0.005 0.051 1209 Dihedral : 5.512 62.124 955 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.26 % Allowed : 5.63 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.27), residues: 869 helix: 0.37 (0.26), residues: 376 sheet: -1.42 (0.35), residues: 181 loop : -2.15 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.009 0.001 HIS B 311 PHE 0.022 0.002 PHE C 344 TYR 0.017 0.002 TYR C 349 ARG 0.004 0.001 ARG B 283 *********************** 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 246 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8317 (mtp85) REVERT: C 234 LEU cc_start: 0.9219 (tt) cc_final: 0.8845 (mt) REVERT: C 250 MET cc_start: 0.8044 (ptm) cc_final: 0.7834 (ptm) REVERT: C 345 ASP cc_start: 0.8471 (m-30) cc_final: 0.7892 (m-30) REVERT: C 346 PHE cc_start: 0.8811 (t80) cc_final: 0.8539 (t80) REVERT: A 18 MET cc_start: 0.8592 (tpp) cc_final: 0.8038 (tpp) REVERT: A 21 ARG cc_start: 0.8668 (ttm170) cc_final: 0.8239 (ttm170) REVERT: A 28 GLU cc_start: 0.8062 (tt0) cc_final: 0.7778 (tm-30) REVERT: A 333 GLN cc_start: 0.8105 (pm20) cc_final: 0.7720 (pm20) REVERT: B 61 MET cc_start: 0.7830 (ppp) cc_final: 0.7615 (ppp) REVERT: B 82 TRP cc_start: 0.7908 (m-10) cc_final: 0.7465 (m-10) REVERT: B 118 ASP cc_start: 0.8274 (p0) cc_final: 0.7934 (p0) REVERT: G 41 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7898 (ttp80) REVERT: G 42 ASP cc_start: 0.8716 (p0) cc_final: 0.7854 (p0) outliers start: 2 outliers final: 0 residues processed: 244 average time/residue: 0.2125 time to fit residues: 67.2496 Evaluate side-chains 184 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN C 325 HIS A 195 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 142 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.112181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091509 restraints weight = 21250.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094313 restraints weight = 12368.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.096204 restraints weight = 8416.245| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7108 Z= 0.181 Angle : 0.658 8.110 9631 Z= 0.347 Chirality : 0.045 0.276 1112 Planarity : 0.004 0.052 1209 Dihedral : 5.331 59.549 955 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % 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: -0.92 (0.28), residues: 869 helix: 0.74 (0.26), residues: 376 sheet: -0.91 (0.36), residues: 179 loop : -2.06 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.022 0.002 PHE A 307 TYR 0.020 0.001 TYR B 145 ARG 0.008 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 262 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 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: C 167 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8245 (mtp85) REVERT: C 234 LEU cc_start: 0.9198 (tt) cc_final: 0.8825 (mt) REVERT: C 250 MET cc_start: 0.8034 (ptm) cc_final: 0.7674 (ptm) REVERT: C 305 ARG cc_start: 0.8827 (mtt90) cc_final: 0.8364 (mtt-85) REVERT: C 327 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8000 (ttp80) REVERT: C 345 ASP cc_start: 0.8469 (m-30) cc_final: 0.7822 (m-30) REVERT: C 346 PHE cc_start: 0.8805 (t80) cc_final: 0.8555 (t80) REVERT: C 357 LEU cc_start: 0.9366 (mt) cc_final: 0.9145 (mt) REVERT: A 22 ASN cc_start: 0.9041 (m110) cc_final: 0.8526 (m110) REVERT: A 28 GLU cc_start: 0.8077 (tt0) cc_final: 0.7771 (tm-30) REVERT: A 204 GLN cc_start: 0.7871 (pp30) cc_final: 0.7493 (pp30) REVERT: A 209 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8207 (ttpp) REVERT: A 333 GLN cc_start: 0.8018 (pm20) cc_final: 0.7799 (pm20) REVERT: B 45 MET cc_start: 0.7844 (mmp) cc_final: 0.7000 (tpp) REVERT: B 61 MET cc_start: 0.7867 (ppp) cc_final: 0.7510 (ppp) REVERT: B 118 ASP cc_start: 0.8246 (p0) cc_final: 0.7955 (p0) REVERT: B 217 MET cc_start: 0.7865 (ttm) cc_final: 0.7650 (ppp) REVERT: B 289 TYR cc_start: 0.7889 (m-80) cc_final: 0.7595 (m-80) REVERT: G 38 GLU cc_start: 0.8388 (tp30) cc_final: 0.6840 (tp30) REVERT: G 41 ARG cc_start: 0.8376 (tmm160) cc_final: 0.7999 (ttp80) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.2170 time to fit residues: 72.8194 Evaluate side-chains 194 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN C 325 HIS A 52 GLN A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 230 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.112259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.092025 restraints weight = 21393.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094528 restraints weight = 13295.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096352 restraints weight = 9488.170| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7108 Z= 0.185 Angle : 0.658 7.263 9631 Z= 0.343 Chirality : 0.045 0.285 1112 Planarity : 0.004 0.052 1209 Dihedral : 5.194 57.156 955 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.26 % Allowed : 3.01 % Favored : 96.73 % 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: -0.67 (0.28), residues: 869 helix: 0.96 (0.27), residues: 372 sheet: -0.74 (0.37), residues: 173 loop : -1.91 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.009 0.001 HIS B 225 PHE 0.020 0.002 PHE C 344 TYR 0.017 0.002 TYR C 349 ARG 0.010 0.001 ARG A 205 *********************** 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 to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 LEU cc_start: 0.9187 (tt) cc_final: 0.8818 (mt) REVERT: C 250 MET cc_start: 0.7983 (ptm) cc_final: 0.7543 (ptm) REVERT: C 345 ASP cc_start: 0.8440 (m-30) cc_final: 0.7889 (m-30) REVERT: C 346 PHE cc_start: 0.8731 (t80) cc_final: 0.8412 (t80) REVERT: C 357 LEU cc_start: 0.9325 (mt) cc_final: 0.9086 (mt) REVERT: A 21 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8300 (ttm170) REVERT: A 28 GLU cc_start: 0.8007 (tt0) cc_final: 0.7793 (tm-30) REVERT: A 209 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8115 (ttpp) REVERT: A 343 ILE cc_start: 0.9255 (tp) cc_final: 0.8837 (tp) REVERT: A 347 ASN cc_start: 0.8404 (m110) cc_final: 0.7994 (m110) REVERT: B 45 MET cc_start: 0.7786 (mmp) cc_final: 0.7085 (mmm) REVERT: B 61 MET cc_start: 0.7831 (ppp) cc_final: 0.7541 (ppp) REVERT: B 118 ASP cc_start: 0.8230 (p0) cc_final: 0.7959 (p0) REVERT: G 41 ARG cc_start: 0.8358 (tmm160) cc_final: 0.8038 (ttp80) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.1887 time to fit residues: 57.9929 Evaluate side-chains 178 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 ASN C 325 HIS A 52 GLN A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 230 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.111488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.091647 restraints weight = 21780.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094222 restraints weight = 13150.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095962 restraints weight = 9176.570| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7108 Z= 0.193 Angle : 0.664 7.812 9631 Z= 0.345 Chirality : 0.045 0.262 1112 Planarity : 0.004 0.051 1209 Dihedral : 5.061 54.788 955 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.39 % Allowed : 3.01 % Favored : 96.60 % 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: -0.47 (0.29), residues: 869 helix: 1.05 (0.26), residues: 375 sheet: -0.77 (0.37), residues: 183 loop : -1.68 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 297 HIS 0.008 0.001 HIS B 225 PHE 0.021 0.002 PHE C 344 TYR 0.020 0.002 TYR C 349 ARG 0.011 0.001 ARG A 205 *********************** 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 242 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 0.731 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 82 ASN cc_start: 0.6766 (m-40) cc_final: 0.6561 (m-40) REVERT: C 161 VAL cc_start: 0.8886 (t) cc_final: 0.8547 (p) REVERT: C 234 LEU cc_start: 0.9155 (tt) cc_final: 0.8800 (mt) REVERT: C 250 MET cc_start: 0.8153 (ptm) cc_final: 0.7712 (ptm) REVERT: C 305 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8368 (mtt-85) REVERT: C 327 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8111 (ttp80) REVERT: C 345 ASP cc_start: 0.8446 (m-30) cc_final: 0.7281 (p0) REVERT: C 346 PHE cc_start: 0.8651 (t80) cc_final: 0.8197 (t80) REVERT: C 357 LEU cc_start: 0.9306 (mt) cc_final: 0.9077 (mt) REVERT: C 364 ILE cc_start: 0.8207 (tt) cc_final: 0.7972 (tp) REVERT: A 22 ASN cc_start: 0.8937 (m110) cc_final: 0.8308 (m110) REVERT: A 37 LEU cc_start: 0.8989 (tp) cc_final: 0.8648 (tt) REVERT: A 195 HIS cc_start: 0.6954 (p90) cc_final: 0.6336 (p-80) REVERT: A 209 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8055 (ttpp) REVERT: B 45 MET cc_start: 0.7786 (mmp) cc_final: 0.7146 (mmt) REVERT: B 61 MET cc_start: 0.7864 (ppp) cc_final: 0.7613 (ppp) REVERT: B 89 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8366 (mtmt) REVERT: B 118 ASP cc_start: 0.8285 (p0) cc_final: 0.8074 (p0) REVERT: B 230 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: B 246 ASP cc_start: 0.8692 (m-30) cc_final: 0.8194 (m-30) outliers start: 3 outliers final: 0 residues processed: 240 average time/residue: 0.1870 time to fit residues: 58.7305 Evaluate side-chains 178 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 63 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 74 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 325 HIS A 331 ASN B 266 HIS ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.108873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088581 restraints weight = 21841.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091090 restraints weight = 13257.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092812 restraints weight = 9286.831| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7108 Z= 0.259 Angle : 0.709 8.253 9631 Z= 0.372 Chirality : 0.046 0.286 1112 Planarity : 0.005 0.050 1209 Dihedral : 5.175 52.701 955 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.29), residues: 869 helix: 1.14 (0.26), residues: 379 sheet: -0.69 (0.38), residues: 182 loop : -1.71 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 135 HIS 0.010 0.001 HIS B 225 PHE 0.021 0.002 PHE C 344 TYR 0.018 0.002 TYR C 349 ARG 0.012 0.001 ARG A 205 *********************** 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 226 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.840 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: C 82 ASN cc_start: 0.6889 (m-40) cc_final: 0.6633 (m-40) REVERT: C 161 VAL cc_start: 0.8913 (t) cc_final: 0.8591 (p) REVERT: C 166 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7549 (tm-30) REVERT: C 234 LEU cc_start: 0.9190 (tt) cc_final: 0.8835 (mt) REVERT: C 250 MET cc_start: 0.8116 (ptm) cc_final: 0.7687 (ptm) REVERT: C 344 PHE cc_start: 0.7894 (t80) cc_final: 0.6733 (t80) REVERT: C 345 ASP cc_start: 0.8468 (m-30) cc_final: 0.7782 (m-30) REVERT: C 346 PHE cc_start: 0.8681 (t80) cc_final: 0.8362 (t80) REVERT: C 348 HIS cc_start: 0.8298 (m-70) cc_final: 0.7833 (m170) REVERT: C 357 LEU cc_start: 0.9320 (mt) cc_final: 0.9099 (mt) REVERT: C 364 ILE cc_start: 0.8185 (tt) cc_final: 0.7913 (tp) REVERT: A 209 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8020 (ttpp) REVERT: A 247 MET cc_start: 0.7480 (mtm) cc_final: 0.7184 (mtm) REVERT: B 45 MET cc_start: 0.7929 (mmp) cc_final: 0.7424 (mmm) REVERT: B 190 LEU cc_start: 0.9128 (tt) cc_final: 0.8705 (tt) REVERT: B 229 ILE cc_start: 0.8626 (pt) cc_final: 0.8394 (pt) REVERT: B 246 ASP cc_start: 0.8609 (m-30) cc_final: 0.8272 (m-30) REVERT: G 37 CYS cc_start: 0.8471 (m) cc_final: 0.8236 (m) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1857 time to fit residues: 55.6474 Evaluate side-chains 168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS A 213 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.105964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085739 restraints weight = 22305.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.088111 restraints weight = 13603.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089735 restraints weight = 9567.849| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7108 Z= 0.333 Angle : 0.774 8.139 9631 Z= 0.405 Chirality : 0.048 0.279 1112 Planarity : 0.005 0.055 1209 Dihedral : 5.536 56.736 955 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.13 % Allowed : 1.44 % 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: -0.48 (0.29), residues: 869 helix: 1.09 (0.26), residues: 376 sheet: -0.74 (0.38), residues: 183 loop : -1.79 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 321 HIS 0.004 0.001 HIS C 348 PHE 0.022 0.002 PHE C 344 TYR 0.020 0.003 TYR C 349 ARG 0.013 0.001 ARG A 205 *********************** 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 210 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.863 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 82 ASN cc_start: 0.6891 (m-40) cc_final: 0.6623 (m-40) REVERT: C 161 VAL cc_start: 0.8935 (t) cc_final: 0.8604 (p) REVERT: C 234 LEU cc_start: 0.9148 (tt) cc_final: 0.8826 (mt) REVERT: C 250 MET cc_start: 0.8161 (ptm) cc_final: 0.7765 (ptm) REVERT: C 345 ASP cc_start: 0.8590 (m-30) cc_final: 0.7685 (p0) REVERT: C 346 PHE cc_start: 0.8717 (t80) cc_final: 0.8339 (t80) REVERT: C 364 ILE cc_start: 0.8349 (tt) cc_final: 0.8077 (tp) REVERT: A 19 ILE cc_start: 0.9240 (tt) cc_final: 0.8938 (tt) REVERT: A 22 ASN cc_start: 0.8997 (m110) cc_final: 0.8407 (m110) REVERT: A 206 SER cc_start: 0.7750 (p) cc_final: 0.7493 (p) REVERT: A 209 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8025 (ttpp) REVERT: B 45 MET cc_start: 0.7730 (mmp) cc_final: 0.7342 (tpp) REVERT: B 89 LYS cc_start: 0.8362 (ptpt) cc_final: 0.8097 (ptpp) REVERT: B 129 ARG cc_start: 0.8602 (ppt170) cc_final: 0.8194 (ttp80) REVERT: B 190 LEU cc_start: 0.9112 (tt) cc_final: 0.8728 (tt) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.1889 time to fit residues: 52.8768 Evaluate side-chains 166 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 0.0670 chunk 68 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS C 348 HIS A 213 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.111556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092010 restraints weight = 21665.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094608 restraints weight = 12958.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096385 restraints weight = 8920.899| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.6124 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= 0.189 Angle : 0.709 8.750 9631 Z= 0.361 Chirality : 0.046 0.238 1112 Planarity : 0.005 0.058 1209 Dihedral : 5.388 70.867 955 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.17 (0.29), residues: 869 helix: 1.29 (0.26), residues: 373 sheet: -0.41 (0.40), residues: 180 loop : -1.63 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.021 0.002 PHE C 344 TYR 0.017 0.002 TYR C 349 ARG 0.014 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 245 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.818 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: 0.8866 (t) cc_final: 0.8500 (p) REVERT: C 234 LEU cc_start: 0.9107 (tt) cc_final: 0.8815 (mt) REVERT: C 238 ILE cc_start: 0.7245 (tt) cc_final: 0.6914 (tt) REVERT: C 250 MET cc_start: 0.8085 (ptm) cc_final: 0.7707 (ptm) REVERT: C 344 PHE cc_start: 0.8114 (t80) cc_final: 0.7041 (t80) REVERT: C 345 ASP cc_start: 0.8488 (m-30) cc_final: 0.7400 (p0) REVERT: C 346 PHE cc_start: 0.8706 (t80) cc_final: 0.8331 (t80) REVERT: C 348 HIS cc_start: 0.8213 (m-70) cc_final: 0.7919 (m170) REVERT: C 357 LEU cc_start: 0.9327 (mt) cc_final: 0.9108 (mt) REVERT: D 13 LEU cc_start: 0.6627 (tp) cc_final: 0.5888 (tp) REVERT: A 19 ILE cc_start: 0.9180 (tt) cc_final: 0.8939 (tt) REVERT: A 22 ASN cc_start: 0.9002 (m110) cc_final: 0.8373 (m110) REVERT: A 197 LYS cc_start: 0.7830 (mptt) cc_final: 0.7493 (mmtt) REVERT: A 209 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7956 (ttpp) REVERT: B 45 MET cc_start: 0.7921 (mmp) cc_final: 0.7410 (tpp) REVERT: B 118 ASP cc_start: 0.8099 (p0) cc_final: 0.7812 (p0) REVERT: B 123 ILE cc_start: 0.9122 (mm) cc_final: 0.8725 (pt) REVERT: B 129 ARG cc_start: 0.8547 (ppt170) cc_final: 0.8153 (ttp80) REVERT: B 190 LEU cc_start: 0.9094 (tt) cc_final: 0.8686 (tt) REVERT: B 253 PHE cc_start: 0.7527 (m-80) cc_final: 0.6056 (m-80) REVERT: B 260 GLU cc_start: 0.7151 (tp30) cc_final: 0.5962 (mp0) REVERT: B 261 LEU cc_start: 0.8447 (tp) cc_final: 0.8244 (tp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1829 time to fit residues: 59.4279 Evaluate side-chains 180 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN C 325 HIS A 255 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.108831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088835 restraints weight = 22237.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091247 restraints weight = 13569.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092930 restraints weight = 9559.058| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7108 Z= 0.236 Angle : 0.713 8.573 9631 Z= 0.369 Chirality : 0.046 0.166 1112 Planarity : 0.005 0.060 1209 Dihedral : 5.342 62.864 955 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % 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: -0.17 (0.29), residues: 869 helix: 1.15 (0.26), residues: 378 sheet: -0.29 (0.40), residues: 178 loop : -1.56 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.019 0.002 PHE B 241 TYR 0.022 0.002 TYR B 85 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 213 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 VAL cc_start: 0.8876 (t) cc_final: 0.8510 (p) REVERT: C 234 LEU cc_start: 0.9123 (tt) cc_final: 0.8813 (mt) REVERT: C 238 ILE cc_start: 0.7185 (tt) cc_final: 0.6862 (tt) REVERT: C 250 MET cc_start: 0.8111 (ptm) cc_final: 0.7699 (ptm) REVERT: C 344 PHE cc_start: 0.7918 (t80) cc_final: 0.6911 (t80) REVERT: C 345 ASP cc_start: 0.8494 (m-30) cc_final: 0.7500 (p0) REVERT: C 346 PHE cc_start: 0.8701 (t80) cc_final: 0.8317 (t80) REVERT: C 357 LEU cc_start: 0.9318 (mt) cc_final: 0.9103 (mt) REVERT: C 364 ILE cc_start: 0.8391 (tt) cc_final: 0.8127 (tp) REVERT: A 19 ILE cc_start: 0.9072 (tt) cc_final: 0.8801 (tt) REVERT: A 22 ASN cc_start: 0.8990 (m110) cc_final: 0.8307 (m110) REVERT: A 197 LYS cc_start: 0.7804 (mptt) cc_final: 0.7464 (mmtt) REVERT: A 209 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7995 (ttpp) REVERT: B 45 MET cc_start: 0.7891 (mmp) cc_final: 0.7301 (mmt) REVERT: B 123 ILE cc_start: 0.9149 (mm) cc_final: 0.8709 (pt) REVERT: B 129 ARG cc_start: 0.8603 (ppt170) cc_final: 0.8186 (ttp80) REVERT: B 190 LEU cc_start: 0.9061 (tt) cc_final: 0.8707 (tt) REVERT: B 260 GLU cc_start: 0.7180 (tp30) cc_final: 0.6227 (mp0) REVERT: B 325 MET cc_start: 0.8267 (mmm) cc_final: 0.8017 (tpp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1758 time to fit residues: 50.5521 Evaluate side-chains 167 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS B 91 HIS B 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.110397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090379 restraints weight = 21769.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092879 restraints weight = 13271.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094580 restraints weight = 9281.892| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7108 Z= 0.211 Angle : 0.728 8.838 9631 Z= 0.374 Chirality : 0.046 0.238 1112 Planarity : 0.005 0.061 1209 Dihedral : 5.258 59.792 955 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.14 (0.29), residues: 869 helix: 1.14 (0.26), residues: 378 sheet: -0.39 (0.40), residues: 178 loop : -1.40 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 339 HIS 0.005 0.001 HIS B 225 PHE 0.028 0.002 PHE B 278 TYR 0.019 0.002 TYR C 349 ARG 0.014 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.40 seconds wall clock time: 45 minutes 13.53 seconds (2713.53 seconds total)