Starting phenix.real_space_refine on Tue Dec 31 19:36:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pso_17858/12_2024/8pso_17858_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pso_17858/12_2024/8pso_17858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pso_17858/12_2024/8pso_17858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pso_17858/12_2024/8pso_17858.map" model { file = "/net/cci-nas-00/data/ceres_data/8pso_17858/12_2024/8pso_17858_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pso_17858/12_2024/8pso_17858_trim.cif" } resolution = 2.4 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= 0.004 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 31 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 5046 2.51 5 N 1459 2.21 5 O 1681 1.98 5 H 7937 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16201 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5036 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: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 476 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: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 969 SG CYS A 161 47.014 44.089 83.490 1.00 27.60 S ATOM 2857 SG CYS A 282 45.317 46.416 86.158 1.00 26.75 S Time building chain proxies: 10.83, per 1000 atoms: 0.67 Number of scatterers: 16201 At special positions: 0 Unit cell: (88.2, 94.92, 102.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 44 16.00 P 31 15.00 Mg 2 11.99 O 1681 8.00 N 1459 7.00 C 5046 6.00 H 7937 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: 4.65 Conformation dependent library (CDL) restraints added in 1.7 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: 41 helices and 10 sheets defined 48.1% alpha, 12.8% beta 7 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 7.54 Creating SS restraints... Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.657A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.540A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 236 removed outlier: 3.585A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.130A 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: 3.626A pdb=" N LEU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.511A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.930A 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 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.579A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 removed outlier: 3.563A pdb=" N GLY B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) 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 204 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.737A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.809A 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 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.979A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 496 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: 3.677A 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: 3.687A 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 Processing helix chain 'C' and resid 100 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.234A 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: 6.234A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.259A 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: 3.726A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 83 removed outlier: 7.242A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 5.39 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: 7915 1.03 - 1.23: 32 1.23 - 1.42: 3521 1.42 - 1.61: 4838 1.61 - 1.81: 64 Bond restraints: 16370 Sorted by residual: bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.94e+00 bond pdb=" C5 CTP F 1 " pdb=" C6 CTP F 1 " ideal model delta sigma weight residual 1.390 1.342 0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C4' CTP F 1 " pdb=" O4' CTP F 1 " ideal model delta sigma weight residual 1.410 1.452 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" C4 CTP F 1 " pdb=" N3 CTP F 1 " ideal model delta sigma weight residual 1.380 1.339 0.041 2.00e-02 2.50e+03 4.24e+00 bond pdb=" C5' CTP F 1 " pdb=" O5' CTP F 1 " ideal model delta sigma weight residual 1.410 1.449 -0.039 2.00e-02 2.50e+03 3.71e+00 ... (remaining 16365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 29524 3.10 - 6.19: 39 6.19 - 9.29: 3 9.29 - 12.38: 4 12.38 - 15.48: 1 Bond angle restraints: 29571 Sorted by residual: angle pdb=" CA PRO B 470 " pdb=" N PRO B 470 " pdb=" CD PRO B 470 " ideal model delta sigma weight residual 112.00 103.06 8.94 1.40e+00 5.10e-01 4.08e+01 angle pdb=" PA CTP F 1 " pdb=" O3A CTP F 1 " pdb=" PB CTP F 1 " ideal model delta sigma weight residual 120.50 135.98 -15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C2' CTP F 1 " pdb=" C3' CTP F 1 " pdb=" C4' CTP F 1 " ideal model delta sigma weight residual 111.00 99.47 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C1' CTP F 1 " pdb=" C2' CTP F 1 " pdb=" C3' CTP F 1 " ideal model delta sigma weight residual 111.00 99.93 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" PB CTP F 1 " pdb=" O3B CTP F 1 " pdb=" PG CTP F 1 " ideal model delta sigma weight residual 120.50 130.57 -10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 29566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 7377 34.72 - 69.44: 317 69.44 - 104.16: 20 104.16 - 138.88: 2 138.88 - 173.61: 2 Dihedral angle restraints: 7718 sinusoidal: 4475 harmonic: 3243 Sorted by residual: dihedral pdb=" O3B CTP F 1 " pdb=" O3A CTP F 1 " pdb=" PB CTP F 1 " pdb=" PA CTP F 1 " ideal model delta sinusoidal sigma weight residual 320.71 153.36 167.34 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1G CTP F 1 " pdb=" O3B CTP F 1 " pdb=" PG CTP F 1 " pdb=" PB CTP F 1 " ideal model delta sinusoidal sigma weight residual 82.72 -47.94 130.65 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O3A CTP F 1 " pdb=" O3B CTP F 1 " pdb=" PB CTP F 1 " pdb=" PG CTP F 1 " ideal model delta sinusoidal sigma weight residual -155.50 -47.76 -107.74 1 2.00e+01 2.50e-03 3.13e+01 ... (remaining 7715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1164 0.050 - 0.100: 129 0.100 - 0.151: 33 0.151 - 0.201: 0 0.201 - 0.251: 1 Chirality restraints: 1327 Sorted by residual: chirality pdb=" C2' CTP F 1 " pdb=" C1' CTP F 1 " pdb=" C3' CTP F 1 " pdb=" O2' CTP F 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' G S 1 " pdb=" C4' G S 1 " pdb=" O3' G S 1 " pdb=" C2' G S 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.14 2.00e-01 2.50e+01 5.14e-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 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1324 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " -0.057 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO B 470 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 162 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A S 8 " -0.022 2.00e-02 2.50e+03 9.61e-03 3.00e+00 pdb=" N9 A S 8 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A S 8 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A S 8 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A S 8 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A S 8 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" H8 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A S 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 537 2.15 - 2.76: 29691 2.76 - 3.37: 46745 3.37 - 3.99: 62048 3.99 - 4.60: 95312 Nonbonded interactions: 234333 Sorted by model distance: nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.532 2.450 nonbonded pdb=" OD2 ASP B 222 " pdb="HH22 ARG B 247 " model vdw 1.614 2.450 nonbonded pdb=" OD1 ASP B 444 " pdb=" H ASP B 444 " model vdw 1.628 2.450 nonbonded pdb=" HZ3 LYS B 249 " pdb=" O CYS B 260 " model vdw 1.637 2.450 nonbonded pdb=" HH TYR B 186 " pdb=" O SER B 286 " model vdw 1.639 2.450 ... (remaining 234328 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=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: 2.590 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: 0.260 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 52.360 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 0.122 8433 Z= 0.170 Angle : 0.562 15.480 11533 Z= 0.274 Chirality : 0.036 0.251 1327 Planarity : 0.005 0.082 1377 Dihedral : 18.686 173.606 3344 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.55 % Allowed : 19.90 % Favored : 78.55 % 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: 1.47 (0.27), residues: 965 helix: 2.12 (0.25), residues: 421 sheet: 0.72 (0.52), residues: 93 loop : -0.03 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 346 HIS 0.003 0.001 HIS A 296 PHE 0.009 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.010 0.000 ARG B 206 *********************** 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 129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.218 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 126 average time/residue: 3.2822 time to fit residues: 434.7067 Evaluate side-chains 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8433 Z= 0.208 Angle : 0.540 8.093 11533 Z= 0.282 Chirality : 0.038 0.158 1327 Planarity : 0.004 0.045 1377 Dihedral : 14.082 166.516 1505 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.43 % Allowed : 18.59 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 965 helix: 2.04 (0.25), residues: 428 sheet: 0.61 (0.52), residues: 95 loop : -0.01 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.006 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.006 0.000 ARG B 206 *********************** 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 131 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.335 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 128 average time/residue: 3.2924 time to fit residues: 443.1985 Evaluate side-chains 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 4.9990 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: 2.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 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 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8433 Z= 0.322 Angle : 0.616 9.367 11533 Z= 0.324 Chirality : 0.041 0.170 1327 Planarity : 0.005 0.049 1377 Dihedral : 13.827 165.429 1499 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.15 % Allowed : 17.64 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 965 helix: 1.61 (0.25), residues: 427 sheet: 0.57 (0.50), residues: 93 loop : -0.23 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 432 HIS 0.006 0.001 HIS A 367 PHE 0.020 0.002 PHE C 44 TYR 0.014 0.002 TYR A 403 ARG 0.005 0.001 ARG B 475 *********************** 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 134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.530 Fit side-chains REVERT: A 332 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8432 (ttp80) outliers start: 18 outliers final: 8 residues processed: 128 average time/residue: 3.3478 time to fit residues: 450.5462 Evaluate side-chains 121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8433 Z= 0.233 Angle : 0.560 8.132 11533 Z= 0.294 Chirality : 0.038 0.150 1327 Planarity : 0.004 0.050 1377 Dihedral : 13.544 164.518 1499 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.55 % Allowed : 18.12 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 965 helix: 1.66 (0.25), residues: 428 sheet: 0.44 (0.50), residues: 95 loop : -0.23 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.006 0.001 HIS A 367 PHE 0.016 0.002 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.005 0.000 ARG B 475 *********************** 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 128 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8439 (ttp80) outliers start: 13 outliers final: 8 residues processed: 123 average time/residue: 3.4736 time to fit residues: 448.5510 Evaluate side-chains 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 LEU 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: 2.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8433 Z= 0.268 Angle : 0.584 8.845 11533 Z= 0.307 Chirality : 0.040 0.159 1327 Planarity : 0.005 0.053 1377 Dihedral : 13.636 164.265 1498 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.67 % Allowed : 18.00 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 965 helix: 1.54 (0.25), residues: 428 sheet: 0.39 (0.50), residues: 95 loop : -0.28 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 432 HIS 0.005 0.001 HIS B 174 PHE 0.018 0.002 PHE C 44 TYR 0.013 0.002 TYR A 403 ARG 0.005 0.000 ARG B 475 *********************** 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 129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.405 Fit side-chains REVERT: A 128 SER cc_start: 0.8662 (t) cc_final: 0.8389 (m) REVERT: A 332 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8453 (ttp80) REVERT: C 82 PHE cc_start: 0.8157 (t80) cc_final: 0.7957 (t80) outliers start: 14 outliers final: 7 residues processed: 124 average time/residue: 3.4368 time to fit residues: 448.2377 Evaluate side-chains 120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8433 Z= 0.238 Angle : 0.566 8.220 11533 Z= 0.297 Chirality : 0.039 0.149 1327 Planarity : 0.005 0.069 1377 Dihedral : 13.607 163.985 1498 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.43 % Allowed : 18.24 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 965 helix: 1.60 (0.25), residues: 428 sheet: 0.39 (0.50), residues: 95 loop : -0.27 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 PHE 0.016 0.002 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG B 475 *********************** 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 125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 128 SER cc_start: 0.8660 (t) cc_final: 0.8377 (m) REVERT: B 486 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7223 (mt) outliers start: 12 outliers final: 7 residues processed: 120 average time/residue: 3.1844 time to fit residues: 402.7313 Evaluate side-chains 121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8433 Z= 0.158 Angle : 0.513 6.838 11533 Z= 0.268 Chirality : 0.037 0.142 1327 Planarity : 0.004 0.068 1377 Dihedral : 13.320 163.590 1497 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.55 % Allowed : 18.24 % Favored : 80.21 % 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: 1.14 (0.27), residues: 965 helix: 1.84 (0.25), residues: 429 sheet: 0.45 (0.51), residues: 95 loop : -0.20 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.011 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.008 0.000 ARG B 475 *********************** 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 125 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8415 (ttp80) outliers start: 13 outliers final: 6 residues processed: 122 average time/residue: 3.4671 time to fit residues: 444.3117 Evaluate side-chains 116 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8433 Z= 0.189 Angle : 0.528 7.447 11533 Z= 0.277 Chirality : 0.037 0.145 1327 Planarity : 0.004 0.068 1377 Dihedral : 13.415 164.010 1497 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.19 % Allowed : 19.07 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 965 helix: 1.81 (0.25), residues: 429 sheet: 0.42 (0.51), residues: 95 loop : -0.21 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.014 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG B 475 *********************** 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 122 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8421 (ttp80) outliers start: 10 outliers final: 5 residues processed: 118 average time/residue: 3.3954 time to fit residues: 423.8540 Evaluate side-chains 116 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0010 chunk 88 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 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: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8433 Z= 0.165 Angle : 0.512 6.985 11533 Z= 0.268 Chirality : 0.037 0.142 1327 Planarity : 0.004 0.065 1377 Dihedral : 13.326 163.741 1497 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.31 % Allowed : 18.83 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 965 helix: 1.89 (0.25), residues: 429 sheet: 0.46 (0.51), residues: 95 loop : -0.18 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG B 475 *********************** 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 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8396 (ttp80) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 3.4100 time to fit residues: 430.3014 Evaluate side-chains 117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8433 Z= 0.201 Angle : 0.536 7.750 11533 Z= 0.281 Chirality : 0.038 0.146 1327 Planarity : 0.004 0.053 1377 Dihedral : 13.457 164.060 1497 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.19 % Allowed : 19.07 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 965 helix: 1.81 (0.25), residues: 429 sheet: 0.44 (0.51), residues: 95 loop : -0.21 (0.28), residues: 441 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 0.015 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG B 475 ********************** 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 121 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.289 Fit side-chains REVERT: B 486 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7199 (mt) outliers start: 10 outliers final: 7 residues processed: 117 average time/residue: 3.3294 time to fit residues: 410.3589 Evaluate side-chains 118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 17 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095015 restraints weight = 22606.057| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.28 r_work: 0.2854 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 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 = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8433 Z= 0.162 Angle : 0.510 6.933 11533 Z= 0.267 Chirality : 0.036 0.142 1327 Planarity : 0.004 0.066 1377 Dihedral : 13.321 163.670 1497 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.19 % Allowed : 18.83 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 965 helix: 1.92 (0.25), residues: 429 sheet: 0.57 (0.52), residues: 93 loop : -0.20 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.009 0.000 ARG B 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7546.20 seconds wall clock time: 134 minutes 53.37 seconds (8093.37 seconds total)