Starting phenix.real_space_refine on Tue Apr 9 10:49:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pso_17858/04_2024/8pso_17858_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pso_17858/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pso_17858/04_2024/8pso_17858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pso_17858/04_2024/8pso_17858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pso_17858/04_2024/8pso_17858_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pso_17858/04_2024/8pso_17858_trim_updated.pdb" } 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 Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 115": "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: 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: 14.78, per 1000 atoms: 0.91 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 - 3.50 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: 14.08 Conformation dependent library (CDL) restraints added in 2.3 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 41.1% alpha, 9.7% beta 7 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 9.65 Creating SS restraints... Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.540A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.585A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.626A pdb=" N LEU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'B' and resid 2 through 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.637A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 182 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.809A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.979A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 454 Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 16 through 23 removed outlier: 3.677A pdb=" N HIS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 54 removed outlier: 5.694A pdb=" N SER C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N CYS C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) 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 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 88 through 97 Processing helix chain 'C' and resid 101 through 106 Processing sheet with id= A, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.433A pdb=" N ALA A 251 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLN A 200 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N TYR A 202 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET A 255 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 241 through 243 Processing sheet with id= C, first strand: chain 'B' and resid 74 through 80 Processing sheet with id= D, 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: 6.317A pdb=" N CYS B 250 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N CYS B 142 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU B 252 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N LEU B 144 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 321 through 323 Processing sheet with id= F, first strand: chain 'B' and resid 326 through 329 Processing sheet with id= G, first strand: chain 'C' and resid 77 through 83 298 hydrogen bonds defined for protein. 813 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: 5.94 Time building geometry restraints manager: 14.63 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: 98.90 - 106.32: 348 106.32 - 113.73: 19522 113.73 - 121.15: 6268 121.15 - 128.56: 3350 128.56 - 135.98: 83 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: 561 2.15 - 2.76: 29745 2.76 - 3.37: 46814 3.37 - 3.99: 62151 3.99 - 4.60: 95432 Nonbonded interactions: 234703 Sorted by model distance: nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.532 1.850 nonbonded pdb=" OD2 ASP B 222 " pdb="HH22 ARG B 247 " model vdw 1.614 1.850 nonbonded pdb=" OD1 ASP B 444 " pdb=" H ASP B 444 " model vdw 1.628 1.850 nonbonded pdb=" HZ3 LYS B 249 " pdb=" O CYS B 260 " model vdw 1.637 1.850 nonbonded pdb=" HH TYR B 186 " pdb=" O SER B 286 " model vdw 1.639 1.850 ... (remaining 234698 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: 2.530 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: 0.250 Extract box with map and model: 6.360 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 76.330 Find NCS groups from input model: 0.330 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.120 ------------------------------------------------------------------------------- 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= 0.183 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 fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.445 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 126 average time/residue: 3.2669 time to fit residues: 433.9088 Evaluate side-chains 123 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.8812 moved from start: 0.0402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8433 Z= 0.202 Angle : 0.520 7.426 11533 Z= 0.268 Chirality : 0.037 0.183 1327 Planarity : 0.004 0.045 1377 Dihedral : 13.777 173.324 1505 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.43 % Allowed : 19.07 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.27), residues: 965 helix: 1.93 (0.25), residues: 421 sheet: 0.53 (0.52), residues: 95 loop : 0.04 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 161 PHE 0.016 0.002 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.005 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 fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: B 444 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.8971 (p0) REVERT: C 100 ASP cc_start: 0.7666 (t0) cc_final: 0.7324 (t0) outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 3.2370 time to fit residues: 440.1615 Evaluate side-chains 122 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 444 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 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: 3.9990 chunk 74 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8808 moved from start: 0.0413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8433 Z= 0.184 Angle : 0.506 7.802 11533 Z= 0.260 Chirality : 0.037 0.149 1327 Planarity : 0.004 0.049 1377 Dihedral : 13.513 170.925 1501 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 1.29 (0.27), residues: 965 helix: 1.86 (0.25), residues: 421 sheet: 0.54 (0.52), residues: 95 loop : 0.02 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS C 28 PHE 0.014 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.005 0.000 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 126 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: B 444 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.9024 (p0) REVERT: C 100 ASP cc_start: 0.7697 (t0) cc_final: 0.7308 (t0) outliers start: 12 outliers final: 6 residues processed: 124 average time/residue: 3.1519 time to fit residues: 411.7055 Evaluate side-chains 120 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 444 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8836 moved from start: 0.0728 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= 0.283 Angle : 0.576 9.258 11533 Z= 0.299 Chirality : 0.040 0.165 1327 Planarity : 0.005 0.051 1377 Dihedral : 13.775 169.660 1501 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.67 % Allowed : 17.76 % Favored : 80.57 % 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: 1.01 (0.27), residues: 965 helix: 1.56 (0.25), residues: 419 sheet: 0.48 (0.51), residues: 95 loop : -0.06 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.019 0.002 PHE C 44 TYR 0.013 0.002 TYR A 403 ARG 0.005 0.001 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 129 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8409 (ttp80) REVERT: B 444 ASP cc_start: 0.9386 (OUTLIER) cc_final: 0.9026 (p0) REVERT: C 100 ASP cc_start: 0.7687 (t0) cc_final: 0.7298 (t0) outliers start: 14 outliers final: 6 residues processed: 125 average time/residue: 3.4019 time to fit residues: 447.4214 Evaluate side-chains 119 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 406 ASP Chi-restraints excluded: chain B residue 444 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=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: 1.9990 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 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: 0.8833 moved from start: 0.0755 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= 0.258 Angle : 0.558 8.538 11533 Z= 0.290 Chirality : 0.039 0.151 1327 Planarity : 0.004 0.054 1377 Dihedral : 13.664 169.022 1500 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.03 % Allowed : 17.52 % Favored : 80.45 % 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: 0.90 (0.26), residues: 965 helix: 1.45 (0.25), residues: 420 sheet: 0.44 (0.50), residues: 95 loop : -0.10 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.017 0.002 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.005 0.001 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 131 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8418 (ttp80) REVERT: B 444 ASP cc_start: 0.9372 (OUTLIER) cc_final: 0.9005 (p0) REVERT: C 100 ASP cc_start: 0.7696 (t0) cc_final: 0.7298 (t0) outliers start: 17 outliers final: 9 residues processed: 124 average time/residue: 3.4178 time to fit residues: 444.4472 Evaluate side-chains 124 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 481 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8840 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 : 0.004 0.034 8433 Z= 0.285 Angle : 0.581 9.215 11533 Z= 0.302 Chirality : 0.040 0.162 1327 Planarity : 0.005 0.070 1377 Dihedral : 13.794 168.895 1500 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.79 % Allowed : 17.76 % Favored : 80.45 % 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: 0.82 (0.26), residues: 965 helix: 1.36 (0.25), residues: 419 sheet: 0.39 (0.50), residues: 95 loop : -0.12 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.019 0.002 PHE C 44 TYR 0.013 0.002 TYR A 403 ARG 0.010 0.001 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 130 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 SER cc_start: 0.8660 (t) cc_final: 0.8376 (m) REVERT: B 444 ASP cc_start: 0.9395 (OUTLIER) cc_final: 0.9036 (p0) REVERT: C 100 ASP cc_start: 0.7676 (t0) cc_final: 0.7280 (t0) outliers start: 15 outliers final: 7 residues processed: 125 average time/residue: 3.3268 time to fit residues: 437.0284 Evaluate side-chains 120 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8821 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8433 Z= 0.196 Angle : 0.522 7.731 11533 Z= 0.271 Chirality : 0.037 0.145 1327 Planarity : 0.004 0.049 1377 Dihedral : 13.560 168.256 1500 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.79 % Allowed : 17.64 % Favored : 80.57 % 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: 0.97 (0.27), residues: 965 helix: 1.53 (0.25), residues: 420 sheet: 0.44 (0.50), residues: 95 loop : -0.08 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS C 28 PHE 0.015 0.002 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.006 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 127 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: B 444 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.8989 (p0) REVERT: C 100 ASP cc_start: 0.7702 (t0) cc_final: 0.7285 (t0) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 3.2997 time to fit residues: 418.2726 Evaluate side-chains 121 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER 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 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 481 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.8828 moved from start: 0.0824 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= 0.220 Angle : 0.540 8.323 11533 Z= 0.280 Chirality : 0.038 0.153 1327 Planarity : 0.004 0.055 1377 Dihedral : 13.643 168.744 1500 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.67 % Allowed : 17.76 % Favored : 80.57 % 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: 0.93 (0.26), residues: 965 helix: 1.48 (0.25), residues: 420 sheet: 0.42 (0.50), residues: 95 loop : -0.08 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.017 0.002 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.006 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 127 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 444 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.9015 (p0) REVERT: C 100 ASP cc_start: 0.7735 (t0) cc_final: 0.7294 (t0) outliers start: 14 outliers final: 9 residues processed: 121 average time/residue: 3.1767 time to fit residues: 404.7309 Evaluate side-chains 121 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 481 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: 1.9990 chunk 88 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.8820 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8433 Z= 0.197 Angle : 0.523 7.792 11533 Z= 0.271 Chirality : 0.037 0.146 1327 Planarity : 0.004 0.052 1377 Dihedral : 13.558 168.412 1500 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.91 % Allowed : 17.52 % Favored : 80.57 % 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 (0.27), residues: 965 helix: 1.55 (0.25), residues: 420 sheet: 0.44 (0.51), residues: 95 loop : -0.07 (0.29), residues: 450 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 0.002 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.006 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 128 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: B 444 ASP cc_start: 0.9345 (OUTLIER) cc_final: 0.9000 (p0) REVERT: C 100 ASP cc_start: 0.7741 (t0) cc_final: 0.7308 (t0) outliers start: 16 outliers final: 10 residues processed: 120 average time/residue: 3.1767 time to fit residues: 401.9190 Evaluate side-chains 121 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER 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 444 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 481 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: 1.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8816 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8433 Z= 0.183 Angle : 0.512 7.597 11533 Z= 0.266 Chirality : 0.037 0.145 1327 Planarity : 0.004 0.052 1377 Dihedral : 13.504 168.555 1500 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.19 % Allowed : 18.24 % Favored : 80.57 % 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: 1.04 (0.27), residues: 965 helix: 1.58 (0.25), residues: 421 sheet: 0.45 (0.51), residues: 95 loop : -0.04 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS C 28 PHE 0.014 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.006 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 fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: C 100 ASP cc_start: 0.7754 (t0) cc_final: 0.7323 (t0) outliers start: 10 outliers final: 7 residues processed: 120 average time/residue: 3.2186 time to fit residues: 407.8887 Evaluate side-chains 117 residues out of total 839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 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 82 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.120655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.094891 restraints weight = 22561.027| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.28 r_work: 0.2860 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 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 = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8433 Z= 0.148 Angle : 0.489 6.762 11533 Z= 0.253 Chirality : 0.036 0.139 1327 Planarity : 0.004 0.050 1377 Dihedral : 13.298 168.650 1498 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.19 % Allowed : 18.36 % Favored : 80.45 % 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: 1.17 (0.27), residues: 965 helix: 1.74 (0.25), residues: 422 sheet: 0.52 (0.52), residues: 95 loop : -0.01 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 346 HIS 0.004 0.001 HIS C 28 PHE 0.011 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.006 0.000 ARG B 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7763.03 seconds wall clock time: 138 minutes 4.37 seconds (8284.37 seconds total)