Starting phenix.real_space_refine on Sun Jan 19 08:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ij0_8094/01_2025/5ij0_8094.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ij0_8094/01_2025/5ij0_8094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ij0_8094/01_2025/5ij0_8094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ij0_8094/01_2025/5ij0_8094.map" model { file = "/net/cci-nas-00/data/ceres_data/5ij0_8094/01_2025/5ij0_8094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ij0_8094/01_2025/5ij0_8094.cif" } resolution = 3.8 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= 0.079 sd= 1.092 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: 7 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 4264 2.51 5 N 1157 2.21 5 O 1306 1.98 5 H 6523 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13304 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 6653 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 6590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6590 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.72, per 1000 atoms: 0.66 Number of scatterers: 13304 At special positions: 0 Unit cell: (75.24, 73.92, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 5 15.00 Mg 1 11.99 O 1306 8.00 N 1157 7.00 C 4264 6.00 H 6523 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 56.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.511A pdb=" N ARG A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.555A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.706A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.979A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.536A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 4.129A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 382 through 401 Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.973A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.561A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.004A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.358A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.997A pdb=" N HIS B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 107 through 126 removed outlier: 4.612A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.554A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.634A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 372 through 391 removed outlier: 4.037A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.163A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.821A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.126A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.604A pdb=" N ALA A 374 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.357A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS B 354 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 374 hydrogen bonds defined for protein. 1071 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: 4.49 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6503 1.03 - 1.23: 29 1.23 - 1.42: 2948 1.42 - 1.61: 3903 1.61 - 1.81: 76 Bond restraints: 13459 Sorted by residual: bond pdb=" CA THR A 51 " pdb=" CB THR A 51 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.56e-02 4.11e+03 3.78e+00 bond pdb=" C HIS A 192 " pdb=" O HIS A 192 " ideal model delta sigma weight residual 1.235 1.257 -0.022 1.26e-02 6.30e+03 3.10e+00 bond pdb=" CA GLN B 11 " pdb=" C GLN B 11 " ideal model delta sigma weight residual 1.524 1.540 -0.016 9.50e-03 1.11e+04 3.01e+00 bond pdb=" C HIS B 190 " pdb=" O HIS B 190 " ideal model delta sigma weight residual 1.236 1.255 -0.019 1.16e-02 7.43e+03 2.80e+00 bond pdb=" C GLU B 111 " pdb=" O GLU B 111 " ideal model delta sigma weight residual 1.236 1.256 -0.019 1.15e-02 7.56e+03 2.80e+00 ... (remaining 13454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 22558 1.34 - 2.68: 1489 2.68 - 4.01: 143 4.01 - 5.35: 30 5.35 - 6.69: 3 Bond angle restraints: 24223 Sorted by residual: angle pdb=" C GLN B 11 " pdb=" CA GLN B 11 " pdb=" CB GLN B 11 " ideal model delta sigma weight residual 117.23 110.54 6.69 1.36e+00 5.41e-01 2.42e+01 angle pdb=" N VAL B 193 " pdb=" CA VAL B 193 " pdb=" C VAL B 193 " ideal model delta sigma weight residual 111.00 105.99 5.01 1.09e+00 8.42e-01 2.12e+01 angle pdb=" N ASN B 195 " pdb=" CA ASN B 195 " pdb=" C ASN B 195 " ideal model delta sigma weight residual 113.23 118.59 -5.36 1.24e+00 6.50e-01 1.87e+01 angle pdb=" C VAL B 286 " pdb=" CA VAL B 286 " pdb=" CB VAL B 286 " ideal model delta sigma weight residual 114.35 109.88 4.47 1.06e+00 8.90e-01 1.78e+01 angle pdb=" N ILE B 356 " pdb=" CA ILE B 356 " pdb=" C ILE B 356 " ideal model delta sigma weight residual 107.55 111.61 -4.06 9.90e-01 1.02e+00 1.68e+01 ... (remaining 24218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.94: 6192 26.94 - 53.87: 161 53.87 - 80.81: 31 80.81 - 107.74: 3 107.74 - 134.68: 2 Dihedral angle restraints: 6389 sinusoidal: 3450 harmonic: 2939 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -156.05 -134.68 1 2.00e+01 2.50e-03 4.09e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -11.85 116.44 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" O2B GDP B 501 " pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " pdb=" PA GDP B 501 " ideal model delta sinusoidal sigma weight residual -180.00 -78.42 -101.58 1 2.00e+01 2.50e-03 2.88e+01 ... (remaining 6386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 712 0.029 - 0.058: 174 0.058 - 0.087: 68 0.087 - 0.117: 55 0.117 - 0.146: 20 Chirality restraints: 1029 Sorted by residual: chirality pdb=" CA ILE A 341 " pdb=" N ILE A 341 " pdb=" C ILE A 341 " pdb=" CB ILE A 341 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 91 " pdb=" N ILE B 91 " pdb=" C ILE B 91 " pdb=" CB ILE B 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1026 not shown) Planarity restraints: 2038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 301 " 0.116 2.00e-02 2.50e+03 1.28e-01 2.46e+02 pdb=" CD GLN A 301 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN A 301 " -0.113 2.00e-02 2.50e+03 pdb=" NE2 GLN A 301 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 301 " 0.192 2.00e-02 2.50e+03 pdb="HE22 GLN A 301 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 256 " 0.115 2.00e-02 2.50e+03 1.25e-01 2.36e+02 pdb=" CD GLN A 256 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 256 " -0.109 2.00e-02 2.50e+03 pdb=" NE2 GLN A 256 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 256 " 0.189 2.00e-02 2.50e+03 pdb="HE22 GLN A 256 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 334 " -0.069 2.00e-02 2.50e+03 7.58e-02 8.63e+01 pdb=" CD GLN B 334 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN B 334 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 GLN B 334 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 334 " -0.113 2.00e-02 2.50e+03 pdb="HE22 GLN B 334 " 0.111 2.00e-02 2.50e+03 ... (remaining 2035 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2053 2.28 - 2.86: 31127 2.86 - 3.44: 35611 3.44 - 4.02: 49183 4.02 - 4.60: 75214 Nonbonded interactions: 193188 Sorted by model distance: nonbonded pdb=" HE ARG B 156 " pdb=" O ASN B 195 " model vdw 1.700 2.450 nonbonded pdb=" O GLY A 143 " pdb=" HG SER A 147 " model vdw 1.722 2.450 nonbonded pdb=" O LEU B 130 " pdb="HH11 ARG B 162 " model vdw 1.724 2.450 nonbonded pdb=" O ALA A 294 " pdb="HD22 ASN A 300 " model vdw 1.724 2.450 nonbonded pdb=" O GLU B 22 " pdb=" HG SER B 25 " model vdw 1.726 2.450 ... (remaining 193183 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: 7.660 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: 0.210 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.330 Find NCS groups from input model: 0.110 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.004 0.030 6936 Z= 0.277 Angle : 0.915 6.691 9418 Z= 0.657 Chirality : 0.040 0.146 1029 Planarity : 0.003 0.027 1224 Dihedral : 11.076 134.678 2538 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.00 % Rotamer: Outliers : 0.41 % Allowed : 0.96 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -2.13 (0.24), residues: 850 helix: -1.45 (0.21), residues: 399 sheet: -0.87 (0.38), residues: 121 loop : -1.33 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 344 HIS 0.002 0.001 HIS A 266 PHE 0.008 0.001 PHE B 20 TYR 0.007 0.001 TYR A 83 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.001 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.8259 (m-30) cc_final: 0.8039 (t0) outliers start: 3 outliers final: 3 residues processed: 147 average time/residue: 0.4840 time to fit residues: 91.0564 Evaluate side-chains 93 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.067115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058628 restraints weight = 73131.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.061589 restraints weight = 28720.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.063486 restraints weight = 14394.935| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6936 Z= 0.187 Angle : 0.574 5.864 9418 Z= 0.309 Chirality : 0.041 0.137 1029 Planarity : 0.005 0.041 1224 Dihedral : 9.441 127.926 960 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 0.82 % Allowed : 6.85 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.59 (0.26), residues: 850 helix: 0.09 (0.24), residues: 408 sheet: -0.46 (0.39), residues: 136 loop : -0.80 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.009 0.001 HIS A 197 PHE 0.009 0.001 PHE A 169 TYR 0.011 0.001 TYR B 159 ARG 0.005 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 1.069 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: 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: B 299 MET cc_start: 0.8864 (mmp) cc_final: 0.8635 (mmp) REVERT: B 325 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8219 (mt-10) REVERT: B 326 VAL cc_start: 0.9605 (t) cc_final: 0.9384 (p) REVERT: B 330 MET cc_start: 0.9025 (mmp) cc_final: 0.8800 (mmp) REVERT: B 363 MET cc_start: 0.7901 (ptm) cc_final: 0.7672 (ptt) outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.4951 time to fit residues: 65.1605 Evaluate side-chains 85 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 131 GLN B 204 ASN B 245 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** 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 = 0.3569 r_free = 0.3569 target = 0.063881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.056032 restraints weight = 77686.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.058767 restraints weight = 30230.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.060519 restraints weight = 15039.632| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6936 Z= 0.250 Angle : 0.577 7.314 9418 Z= 0.310 Chirality : 0.041 0.132 1029 Planarity : 0.005 0.070 1224 Dihedral : 9.306 123.856 960 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.82 % Rotamer: Outliers : 0.96 % Allowed : 7.67 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.28), residues: 850 helix: 0.49 (0.24), residues: 406 sheet: -0.50 (0.40), residues: 152 loop : -0.53 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 397 HIS 0.007 0.001 HIS B 28 PHE 0.016 0.001 PHE B 20 TYR 0.017 0.002 TYR A 224 ARG 0.007 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.076 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: A 24 TYR cc_start: 0.8005 (m-10) cc_final: 0.7750 (m-10) REVERT: A 282 TYR cc_start: 0.9208 (m-80) cc_final: 0.8869 (m-80) REVERT: B 325 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 326 VAL cc_start: 0.9649 (t) cc_final: 0.9442 (p) outliers start: 7 outliers final: 5 residues processed: 85 average time/residue: 0.4076 time to fit residues: 46.9555 Evaluate side-chains 77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 59 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.062378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054073 restraints weight = 77164.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056745 restraints weight = 30889.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.058480 restraints weight = 15960.790| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6936 Z= 0.227 Angle : 0.552 5.888 9418 Z= 0.295 Chirality : 0.041 0.139 1029 Planarity : 0.004 0.044 1224 Dihedral : 9.116 130.626 957 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.71 % Rotamer: Outliers : 0.96 % Allowed : 9.32 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 850 helix: 0.78 (0.24), residues: 404 sheet: -0.28 (0.41), residues: 152 loop : -0.45 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.003 0.001 HIS A 283 PHE 0.011 0.001 PHE B 20 TYR 0.011 0.001 TYR A 224 ARG 0.005 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8054 (m-10) cc_final: 0.7781 (m-10) REVERT: A 282 TYR cc_start: 0.9248 (m-80) cc_final: 0.8877 (m-80) REVERT: B 323 MET cc_start: 0.8766 (mmm) cc_final: 0.8284 (mmm) outliers start: 7 outliers final: 6 residues processed: 85 average time/residue: 0.4131 time to fit residues: 47.6332 Evaluate side-chains 77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.061996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054268 restraints weight = 79570.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.056900 restraints weight = 31266.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.058519 restraints weight = 15797.008| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6936 Z= 0.238 Angle : 0.558 7.042 9418 Z= 0.297 Chirality : 0.041 0.137 1029 Planarity : 0.004 0.044 1224 Dihedral : 9.093 133.495 957 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.00 % Rotamer: Outliers : 1.51 % Allowed : 10.14 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.34 (0.29), residues: 850 helix: 0.98 (0.25), residues: 404 sheet: -0.18 (0.41), residues: 152 loop : -0.45 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 397 HIS 0.004 0.001 HIS A 283 PHE 0.013 0.001 PHE B 20 TYR 0.017 0.001 TYR A 83 ARG 0.005 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.7934 (m-10) cc_final: 0.7641 (m-10) REVERT: A 282 TYR cc_start: 0.9150 (m-80) cc_final: 0.8777 (m-80) REVERT: B 323 MET cc_start: 0.8684 (mmm) cc_final: 0.8329 (mmm) REVERT: B 403 MET cc_start: 0.7636 (mmm) cc_final: 0.7390 (mmm) outliers start: 11 outliers final: 8 residues processed: 84 average time/residue: 0.4801 time to fit residues: 54.0996 Evaluate side-chains 80 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.061862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.053876 restraints weight = 78938.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056497 restraints weight = 31253.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.058168 restraints weight = 15917.115| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6936 Z= 0.196 Angle : 0.528 5.791 9418 Z= 0.278 Chirality : 0.041 0.138 1029 Planarity : 0.004 0.082 1224 Dihedral : 9.186 134.646 957 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 1.10 % Allowed : 10.96 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.26 (0.29), residues: 850 helix: 0.96 (0.25), residues: 416 sheet: -0.13 (0.41), residues: 147 loop : -0.69 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.006 0.001 HIS A 107 PHE 0.014 0.001 PHE B 20 TYR 0.012 0.001 TYR A 83 ARG 0.008 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.161 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: A 24 TYR cc_start: 0.7923 (m-10) cc_final: 0.7607 (m-10) REVERT: A 282 TYR cc_start: 0.9229 (m-80) cc_final: 0.8850 (m-80) REVERT: B 323 MET cc_start: 0.8648 (mmm) cc_final: 0.8224 (mmm) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.4150 time to fit residues: 46.3347 Evaluate side-chains 73 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 30 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 10 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.060950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.053171 restraints weight = 79825.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055759 restraints weight = 31487.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.057403 restraints weight = 15968.298| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6936 Z= 0.207 Angle : 0.537 5.860 9418 Z= 0.282 Chirality : 0.041 0.143 1029 Planarity : 0.004 0.053 1224 Dihedral : 9.216 138.341 956 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.88 % Favored : 95.88 % Rotamer: Outliers : 0.96 % Allowed : 11.92 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.29), residues: 850 helix: 1.01 (0.25), residues: 417 sheet: -0.07 (0.42), residues: 147 loop : -0.73 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.003 0.001 HIS A 283 PHE 0.025 0.001 PHE B 133 TYR 0.011 0.001 TYR A 83 ARG 0.005 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.977 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: A 24 TYR cc_start: 0.7848 (m-10) cc_final: 0.7593 (m-10) REVERT: A 282 TYR cc_start: 0.9160 (m-80) cc_final: 0.8817 (m-80) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.4086 time to fit residues: 45.3740 Evaluate side-chains 75 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 43 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.061284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.053264 restraints weight = 80746.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.055833 restraints weight = 32465.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057477 restraints weight = 16760.387| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6936 Z= 0.241 Angle : 0.553 6.309 9418 Z= 0.293 Chirality : 0.041 0.141 1029 Planarity : 0.004 0.049 1224 Dihedral : 9.502 145.678 956 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.76 % Favored : 96.00 % Rotamer: Outliers : 1.10 % Allowed : 11.51 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.21 (0.29), residues: 850 helix: 0.87 (0.25), residues: 423 sheet: -0.08 (0.42), residues: 147 loop : -0.71 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 21 HIS 0.004 0.001 HIS A 283 PHE 0.011 0.001 PHE B 20 TYR 0.011 0.001 TYR B 159 ARG 0.006 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.043 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 outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.3925 time to fit residues: 41.8303 Evaluate side-chains 78 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 414 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.062222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054316 restraints weight = 78569.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056948 restraints weight = 30976.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.058591 restraints weight = 15717.175| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6936 Z= 0.157 Angle : 0.527 6.805 9418 Z= 0.272 Chirality : 0.041 0.135 1029 Planarity : 0.004 0.045 1224 Dihedral : 9.464 147.457 956 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.82 % Favored : 96.94 % Rotamer: Outliers : 0.82 % Allowed : 12.33 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.56 (0.29), residues: 850 helix: 1.25 (0.25), residues: 413 sheet: -0.01 (0.43), residues: 147 loop : -0.58 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 21 HIS 0.003 0.001 HIS B 264 PHE 0.015 0.001 PHE B 20 TYR 0.009 0.001 TYR A 172 ARG 0.004 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 1.188 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: A 24 TYR cc_start: 0.7773 (m-10) cc_final: 0.7517 (m-10) REVERT: A 36 MET cc_start: 0.7815 (ptm) cc_final: 0.7497 (ppp) outliers start: 6 outliers final: 6 residues processed: 83 average time/residue: 0.4633 time to fit residues: 50.8802 Evaluate side-chains 80 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.062409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.054540 restraints weight = 78622.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.057226 restraints weight = 30627.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.058893 restraints weight = 15326.849| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6936 Z= 0.142 Angle : 0.525 7.818 9418 Z= 0.266 Chirality : 0.041 0.138 1029 Planarity : 0.004 0.043 1224 Dihedral : 9.300 146.413 956 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.82 % Favored : 96.94 % Rotamer: Outliers : 0.55 % Allowed : 12.60 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.72 (0.29), residues: 850 helix: 1.41 (0.25), residues: 412 sheet: 0.13 (0.44), residues: 147 loop : -0.60 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.003 0.001 HIS B 6 PHE 0.015 0.001 PHE B 20 TYR 0.008 0.001 TYR A 172 ARG 0.003 0.000 ARG B 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.041 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: A 24 TYR cc_start: 0.7766 (m-10) cc_final: 0.7473 (m-10) REVERT: A 36 MET cc_start: 0.7834 (ptm) cc_final: 0.7489 (ppp) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.4616 time to fit residues: 50.9708 Evaluate side-chains 77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8246 > 50: distance: 39 - 44: 25.370 distance: 44 - 45: 24.518 distance: 44 - 52: 34.822 distance: 45 - 46: 17.288 distance: 45 - 48: 6.514 distance: 45 - 53: 22.787 distance: 46 - 47: 16.192 distance: 46 - 63: 21.577 distance: 48 - 49: 17.128 distance: 48 - 50: 16.294 distance: 48 - 54: 23.011 distance: 49 - 51: 7.528 distance: 49 - 55: 7.805 distance: 49 - 56: 10.277 distance: 50 - 57: 12.818 distance: 50 - 58: 6.164 distance: 50 - 59: 7.426 distance: 51 - 60: 5.204 distance: 51 - 61: 3.427 distance: 51 - 62: 7.090 distance: 63 - 64: 7.124 distance: 63 - 72: 9.480 distance: 64 - 65: 15.153 distance: 64 - 67: 16.456 distance: 64 - 73: 17.538 distance: 65 - 66: 35.560 distance: 65 - 80: 33.970 distance: 67 - 68: 40.807 distance: 67 - 74: 15.444 distance: 67 - 75: 41.001 distance: 68 - 69: 19.664 distance: 68 - 76: 21.808 distance: 68 - 77: 15.357 distance: 69 - 70: 3.320 distance: 69 - 71: 8.960 distance: 71 - 78: 4.277 distance: 71 - 79: 4.600 distance: 80 - 81: 22.595 distance: 80 - 86: 29.892 distance: 81 - 82: 9.102 distance: 81 - 84: 34.194 distance: 81 - 87: 35.744 distance: 82 - 83: 9.025 distance: 82 - 94: 13.050 distance: 84 - 85: 31.116 distance: 84 - 88: 37.616 distance: 84 - 89: 31.536 distance: 85 - 86: 30.007 distance: 85 - 90: 23.695 distance: 85 - 91: 6.715 distance: 86 - 92: 40.743 distance: 86 - 93: 18.161 distance: 94 - 95: 7.269 distance: 94 - 102: 10.166 distance: 95 - 96: 18.580 distance: 95 - 98: 12.561 distance: 95 - 103: 26.396 distance: 96 - 97: 13.634 distance: 96 - 106: 17.838 distance: 98 - 99: 22.140 distance: 98 - 104: 17.528 distance: 98 - 105: 20.139 distance: 99 - 100: 13.604 distance: 99 - 101: 19.842 distance: 106 - 107: 20.904 distance: 106 - 110: 41.585 distance: 107 - 108: 11.498 distance: 107 - 111: 18.639 distance: 107 - 112: 17.619 distance: 108 - 109: 18.963 distance: 108 - 113: 23.508 distance: 113 - 114: 17.901 distance: 113 - 122: 20.478 distance: 114 - 115: 13.127 distance: 114 - 117: 18.484 distance: 114 - 123: 14.915 distance: 115 - 116: 19.283 distance: 115 - 130: 27.825 distance: 117 - 118: 23.491 distance: 117 - 124: 17.316 distance: 117 - 125: 19.642 distance: 118 - 119: 3.087 distance: 118 - 126: 10.673 distance: 118 - 127: 7.200 distance: 119 - 120: 12.157 distance: 119 - 121: 11.222 distance: 121 - 128: 3.555 distance: 121 - 129: 4.783 distance: 130 - 131: 6.942 distance: 130 - 138: 8.611 distance: 131 - 132: 4.183 distance: 131 - 134: 9.912 distance: 131 - 139: 9.469 distance: 132 - 133: 9.254 distance: 132 - 147: 11.358 distance: 134 - 135: 7.499 distance: 134 - 140: 14.893 distance: 134 - 141: 20.142 distance: 135 - 136: 5.958 distance: 135 - 142: 4.163 distance: 135 - 143: 7.965 distance: 136 - 137: 5.895 distance: 137 - 146: 3.075 distance: 147 - 148: 3.296 distance: 147 - 153: 3.099 distance: 148 - 149: 3.909 distance: 148 - 154: 3.425 distance: 149 - 150: 3.648 distance: 151 - 155: 4.261 distance: 151 - 156: 4.158 distance: 153 - 159: 3.499 distance: 153 - 160: 6.433 distance: 161 - 162: 11.358 distance: 162 - 163: 5.234 distance: 162 - 166: 10.396 distance: 162 - 167: 9.512 distance: 163 - 164: 5.141 distance: 163 - 168: 18.847 distance: 168 - 169: 13.440 distance: 168 - 176: 30.535 distance: 169 - 170: 27.904 distance: 169 - 172: 12.340 distance: 169 - 177: 31.034 distance: 170 - 171: 43.543 distance: 170 - 180: 27.090 distance: 171 - 200: 25.378 distance: 172 - 173: 8.690 distance: 172 - 178: 16.397 distance: 172 - 179: 9.138 distance: 173 - 174: 16.632 distance: 173 - 175: 15.780