Starting phenix.real_space_refine on Tue Apr 9 10:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psu_17862/04_2024/8psu_17862.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psu_17862/04_2024/8psu_17862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psu_17862/04_2024/8psu_17862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psu_17862/04_2024/8psu_17862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psu_17862/04_2024/8psu_17862.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psu_17862/04_2024/8psu_17862.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 29 5.49 5 S 44 5.16 5 C 5047 2.51 5 N 1461 2.21 5 O 1630 1.98 5 H 7957 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16169 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5035 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "B" Number of atoms: 7974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Conformer: "B" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} bond proxies already assigned to first conformer: 8044 Chain: "C" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2233 Classifications: {'peptide': 140} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "V" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 440 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 8} Chain: "S" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 486 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 968 SG CYS A 161 53.348 48.182 17.600 1.00 42.34 S ATOM 2856 SG CYS A 282 52.801 45.100 15.249 1.00 54.27 S Time building chain proxies: 10.50, per 1000 atoms: 0.65 Number of scatterers: 16169 At special positions: 0 Unit cell: (86.9, 97.9, 103.4, 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) Zn 1 29.99 S 44 16.00 P 29 15.00 O 1630 8.00 N 1461 7.00 C 5047 6.00 H 7957 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.65 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " Number of angles added : 2 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 47.3% alpha, 12.8% beta 7 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 6.60 Creating SS restraints... Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.679A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.703A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 236 removed outlier: 3.662A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.544A pdb=" N LEU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.558A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.947A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.731A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.911A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 161 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 236 through 248 removed outlier: 3.714A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.035A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.906A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.972A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.504A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.558A pdb=" N HIS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.552A pdb=" N ASP C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 87 through 98 removed outlier: 3.522A pdb=" N GLY C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.589A pdb=" N THR B 293 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.102A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.102A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.798A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA8, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 83 removed outlier: 7.099A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 12.23 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: 7935 1.03 - 1.23: 33 1.23 - 1.42: 3529 1.42 - 1.61: 4825 1.61 - 1.81: 64 Bond restraints: 16386 Sorted by residual: bond pdb=" C LEU B 144 " pdb=" N ARG B 145 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.46e-02 4.69e+03 1.15e+01 bond pdb=" C ARG B 145 " pdb=" N ASP B 146 " ideal model delta sigma weight residual 1.327 1.302 0.025 1.47e-02 4.63e+03 2.94e+00 bond pdb=" C VAL B 170 " pdb=" O VAL B 170 " ideal model delta sigma weight residual 1.237 1.246 -0.010 1.13e-02 7.83e+03 7.17e-01 bond pdb=" CB ARG A 189 " pdb=" CG ARG A 189 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.23e-01 bond pdb=" C LEU B 166 " pdb=" O LEU B 166 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.22e-01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.80: 378 106.80 - 113.60: 19455 113.60 - 120.40: 5253 120.40 - 127.20: 4390 127.20 - 134.00: 136 Bond angle restraints: 29612 Sorted by residual: angle pdb=" N ASP A 380 " pdb=" CA ASP A 380 " pdb=" CB ASP A 380 " ideal model delta sigma weight residual 113.65 110.09 3.56 1.47e+00 4.63e-01 5.87e+00 angle pdb=" C PHE B 287 " pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.04e+00 angle pdb=" O ARG B 145 " pdb=" C ARG B 145 " pdb=" N ASP B 146 " ideal model delta sigma weight residual 123.22 121.06 2.16 1.14e+00 7.69e-01 3.58e+00 angle pdb=" CA ARG B 145 " pdb=" C ARG B 145 " pdb=" N ASP B 146 " ideal model delta sigma weight residual 116.37 118.68 -2.31 1.23e+00 6.61e-01 3.51e+00 angle pdb=" CB ARG A 189 " pdb=" CG ARG A 189 " pdb=" CD ARG A 189 " ideal model delta sigma weight residual 111.30 115.20 -3.90 2.30e+00 1.89e-01 2.87e+00 ... (remaining 29607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6777 17.94 - 35.88: 640 35.88 - 53.82: 234 53.82 - 71.77: 60 71.77 - 89.71: 14 Dihedral angle restraints: 7725 sinusoidal: 4483 harmonic: 3242 Sorted by residual: dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual 180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" O4' U V 10 " pdb=" C1' U V 10 " pdb=" N1 U V 10 " pdb=" C2 U V 10 " ideal model delta sinusoidal sigma weight residual -128.00 -176.52 48.52 1 1.70e+01 3.46e-03 1.12e+01 dihedral pdb=" CB GLU A 326 " pdb=" CG GLU A 326 " pdb=" CD GLU A 326 " pdb=" OE1 GLU A 326 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 871 0.028 - 0.056: 342 0.056 - 0.084: 57 0.084 - 0.112: 44 0.112 - 0.140: 14 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA ILE B 253 " pdb=" N ILE B 253 " pdb=" C ILE B 253 " pdb=" CB ILE B 253 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL B 417 " pdb=" N VAL B 417 " pdb=" C VAL B 417 " pdb=" CB VAL B 417 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1325 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 162 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.021 2.00e-02 2.50e+03 8.36e-03 2.27e+00 pdb=" N9 A V 4 " -0.019 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" H8 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 470 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.019 5.00e-02 4.00e+02 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 945 2.19 - 2.79: 31731 2.79 - 3.40: 43845 3.40 - 4.00: 58522 4.00 - 4.60: 91055 Nonbonded interactions: 226098 Sorted by model distance: nonbonded pdb=" HH TYR B 186 " pdb=" O SER B 286 " model vdw 1.589 1.850 nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.605 1.850 nonbonded pdb=" O PHE B 164 " pdb=" HG SER B 168 " model vdw 1.630 1.850 nonbonded pdb=" O GLY A 309 " pdb="HH22 ARG B 394 " model vdw 1.651 1.850 nonbonded pdb=" HG SER C 121 " pdb=" OD1 ASP C 125 " model vdw 1.658 1.850 ... (remaining 226093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.220 Extract box with map and model: 3.050 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 63.640 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.003 0.049 8429 Z= 0.162 Angle : 0.446 4.533 11527 Z= 0.235 Chirality : 0.035 0.140 1328 Planarity : 0.003 0.048 1376 Dihedral : 17.338 89.707 3348 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.18 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 16.45 % Favored : 83.55 % 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: 1.54 (0.28), residues: 965 helix: 2.19 (0.26), residues: 432 sheet: -0.05 (0.51), residues: 103 loop : 0.16 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 346 HIS 0.003 0.001 HIS B 208 PHE 0.009 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.002 0.000 ARG B 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.7080 time to fit residues: 81.6842 Evaluate side-chains 89 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8429 Z= 0.251 Angle : 0.482 4.621 11527 Z= 0.252 Chirality : 0.037 0.158 1328 Planarity : 0.004 0.051 1376 Dihedral : 12.207 74.130 1498 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.28 % Favored : 97.51 % Rotamer: Outliers : 0.95 % Allowed : 15.97 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 965 helix: 2.13 (0.26), residues: 434 sheet: 0.04 (0.52), residues: 103 loop : 0.05 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.246 Fit side-chains REVERT: B 224 ASP cc_start: 0.8419 (m-30) cc_final: 0.8197 (m-30) outliers start: 8 outliers final: 5 residues processed: 96 average time/residue: 0.6530 time to fit residues: 78.9566 Evaluate side-chains 95 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8429 Z= 0.340 Angle : 0.518 4.720 11527 Z= 0.273 Chirality : 0.038 0.163 1328 Planarity : 0.004 0.055 1376 Dihedral : 12.318 74.759 1498 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.28 % Favored : 97.51 % Rotamer: Outliers : 1.55 % Allowed : 15.61 % Favored : 82.84 % 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: 1.05 (0.27), residues: 965 helix: 1.78 (0.25), residues: 434 sheet: 0.02 (0.51), residues: 103 loop : -0.19 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.006 0.001 HIS B 174 PHE 0.011 0.001 PHE B 4 TYR 0.014 0.002 TYR A 403 ARG 0.003 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.254 Fit side-chains REVERT: A 245 ASP cc_start: 0.7565 (m-30) cc_final: 0.7221 (m-30) REVERT: B 216 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8561 (mmtp) REVERT: B 224 ASP cc_start: 0.8395 (m-30) cc_final: 0.8167 (m-30) REVERT: B 461 ARG cc_start: 0.7783 (ttm110) cc_final: 0.6525 (mpp80) REVERT: C 3 GLN cc_start: 0.5858 (mm-40) cc_final: 0.5615 (mm110) REVERT: C 90 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7904 (mt-10) outliers start: 13 outliers final: 8 residues processed: 104 average time/residue: 0.6559 time to fit residues: 87.5637 Evaluate side-chains 102 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8429 Z= 0.165 Angle : 0.445 4.517 11527 Z= 0.233 Chirality : 0.035 0.153 1328 Planarity : 0.004 0.049 1376 Dihedral : 12.169 74.284 1498 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.97 % Favored : 97.82 % Rotamer: Outliers : 1.07 % Allowed : 15.85 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 965 helix: 2.06 (0.25), residues: 435 sheet: 0.12 (0.52), residues: 103 loop : -0.05 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.008 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.001 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.234 Fit side-chains REVERT: B 224 ASP cc_start: 0.8364 (m-30) cc_final: 0.8136 (m-30) REVERT: B 461 ARG cc_start: 0.7769 (ttm110) cc_final: 0.6498 (mpp80) REVERT: C 3 GLN cc_start: 0.5751 (mm-40) cc_final: 0.5530 (mm110) REVERT: C 13 GLU cc_start: 0.7054 (pt0) cc_final: 0.6727 (pt0) REVERT: C 55 ASP cc_start: 0.7678 (t0) cc_final: 0.6881 (m-30) REVERT: C 88 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: C 90 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7888 (mt-10) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.6233 time to fit residues: 83.3852 Evaluate side-chains 100 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8429 Z= 0.215 Angle : 0.459 4.559 11527 Z= 0.241 Chirality : 0.036 0.155 1328 Planarity : 0.004 0.051 1376 Dihedral : 12.167 74.430 1498 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.28 % Favored : 97.51 % Rotamer: Outliers : 1.31 % Allowed : 15.61 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 965 helix: 2.04 (0.25), residues: 434 sheet: 0.08 (0.52), residues: 103 loop : -0.11 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.002 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.134 Fit side-chains REVERT: B 224 ASP cc_start: 0.8373 (m-30) cc_final: 0.8148 (m-30) REVERT: B 461 ARG cc_start: 0.7783 (ttm110) cc_final: 0.6515 (mpp80) REVERT: C 13 GLU cc_start: 0.7095 (pt0) cc_final: 0.6762 (pt0) REVERT: C 88 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: C 90 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7905 (mt-10) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.6495 time to fit residues: 82.4818 Evaluate side-chains 102 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8429 Z= 0.241 Angle : 0.471 4.595 11527 Z= 0.248 Chirality : 0.036 0.156 1328 Planarity : 0.004 0.051 1376 Dihedral : 12.204 74.475 1498 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.38 % Favored : 97.41 % Rotamer: Outliers : 1.43 % Allowed : 16.09 % Favored : 82.48 % 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: 1.22 (0.27), residues: 965 helix: 1.96 (0.25), residues: 435 sheet: 0.02 (0.52), residues: 103 loop : -0.14 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.002 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.190 Fit side-chains REVERT: B 224 ASP cc_start: 0.8374 (m-30) cc_final: 0.8152 (m-30) REVERT: B 461 ARG cc_start: 0.7804 (ttm110) cc_final: 0.6545 (mpp80) REVERT: C 13 GLU cc_start: 0.7242 (pt0) cc_final: 0.6902 (pt0) REVERT: C 88 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: C 90 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7859 (mt-10) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.6553 time to fit residues: 83.6524 Evaluate side-chains 103 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8429 Z= 0.185 Angle : 0.448 4.535 11527 Z= 0.235 Chirality : 0.035 0.152 1328 Planarity : 0.004 0.050 1376 Dihedral : 12.144 74.324 1498 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.28 % Favored : 97.51 % Rotamer: Outliers : 1.31 % Allowed : 16.45 % Favored : 82.24 % 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: 1.35 (0.27), residues: 965 helix: 2.09 (0.25), residues: 435 sheet: 0.09 (0.52), residues: 103 loop : -0.10 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.008 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.002 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.315 Fit side-chains REVERT: B 224 ASP cc_start: 0.8368 (m-30) cc_final: 0.8149 (m-30) REVERT: C 13 GLU cc_start: 0.7210 (pt0) cc_final: 0.6843 (pt0) REVERT: C 55 ASP cc_start: 0.7593 (t0) cc_final: 0.6684 (m-30) REVERT: C 88 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: C 90 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7858 (mt-10) outliers start: 11 outliers final: 10 residues processed: 103 average time/residue: 0.6340 time to fit residues: 83.1673 Evaluate side-chains 104 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8429 Z= 0.145 Angle : 0.431 4.472 11527 Z= 0.225 Chirality : 0.035 0.149 1328 Planarity : 0.003 0.049 1376 Dihedral : 12.042 74.202 1498 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.97 % Favored : 97.82 % Rotamer: Outliers : 0.95 % Allowed : 16.92 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.28), residues: 965 helix: 2.29 (0.26), residues: 435 sheet: 0.15 (0.52), residues: 103 loop : -0.03 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.002 0.000 HIS B 378 PHE 0.008 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.002 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.398 Fit side-chains REVERT: B 461 ARG cc_start: 0.7771 (ttm110) cc_final: 0.6459 (mpp80) REVERT: C 13 GLU cc_start: 0.7273 (pt0) cc_final: 0.6944 (pt0) REVERT: C 55 ASP cc_start: 0.7542 (t0) cc_final: 0.6681 (m-30) REVERT: C 88 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7417 (mp10) outliers start: 8 outliers final: 7 residues processed: 102 average time/residue: 0.6301 time to fit residues: 81.6015 Evaluate side-chains 102 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8429 Z= 0.275 Angle : 0.486 4.632 11527 Z= 0.256 Chirality : 0.037 0.157 1328 Planarity : 0.004 0.052 1376 Dihedral : 12.167 74.475 1498 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.80 % Favored : 96.99 % Rotamer: Outliers : 1.19 % Allowed : 16.92 % Favored : 81.88 % 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: 1.24 (0.27), residues: 965 helix: 2.03 (0.25), residues: 434 sheet: 0.02 (0.51), residues: 103 loop : -0.19 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.002 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.307 Fit side-chains REVERT: A 323 ASP cc_start: 0.8375 (t70) cc_final: 0.8041 (t70) REVERT: C 13 GLU cc_start: 0.7283 (pt0) cc_final: 0.6965 (pt0) REVERT: C 55 ASP cc_start: 0.7518 (t0) cc_final: 0.6594 (m-30) REVERT: C 88 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7415 (mp10) outliers start: 10 outliers final: 9 residues processed: 101 average time/residue: 0.6262 time to fit residues: 80.4173 Evaluate side-chains 102 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8429 Z= 0.140 Angle : 0.437 4.463 11527 Z= 0.229 Chirality : 0.035 0.149 1328 Planarity : 0.003 0.048 1376 Dihedral : 12.085 74.170 1498 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.76 % Favored : 98.03 % Rotamer: Outliers : 0.95 % Allowed : 17.16 % Favored : 81.88 % 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: 1.52 (0.28), residues: 965 helix: 2.26 (0.26), residues: 435 sheet: 0.14 (0.51), residues: 103 loop : -0.04 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.002 0.000 HIS B 378 PHE 0.008 0.001 PHE A 313 TYR 0.009 0.001 TYR A 403 ARG 0.002 0.000 ARG C 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.386 Fit side-chains REVERT: C 13 GLU cc_start: 0.7298 (pt0) cc_final: 0.6987 (pt0) REVERT: C 55 ASP cc_start: 0.7560 (t0) cc_final: 0.6666 (m-30) REVERT: C 88 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7410 (mp10) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.6531 time to fit residues: 83.0655 Evaluate side-chains 99 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.095869 restraints weight = 29996.190| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.65 r_work: 0.2875 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8429 Z= 0.156 Angle : 0.436 4.482 11527 Z= 0.228 Chirality : 0.035 0.150 1328 Planarity : 0.003 0.050 1376 Dihedral : 12.037 74.213 1498 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.18 % Favored : 97.62 % Rotamer: Outliers : 0.83 % Allowed : 17.28 % Favored : 81.88 % 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: 1.57 (0.28), residues: 965 helix: 2.30 (0.26), residues: 435 sheet: 0.16 (0.52), residues: 103 loop : 0.00 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS B 378 PHE 0.009 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.002 0.000 ARG C 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4199.36 seconds wall clock time: 75 minutes 30.19 seconds (4530.19 seconds total)