Starting phenix.real_space_refine on Tue Jul 23 02:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/07_2024/8pt6_17868_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/07_2024/8pt6_17868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/07_2024/8pt6_17868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/07_2024/8pt6_17868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/07_2024/8pt6_17868_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt6_17868/07_2024/8pt6_17868_neut_trim.cif" } resolution = 3.03 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= 0.001 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 3 6.06 5 P 31 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6433 2.51 5 N 1828 2.21 5 O 2025 1.98 5 H 10051 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20436 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7971 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 7970 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Conformer: "B" Number of residues, atoms: 515, 7970 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} bond proxies already assigned to first conformer: 8041 Chain: "C" Number of atoms: 4887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4887 Classifications: {'peptide': 310} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 1 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: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 486 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 44.562 50.821 17.982 1.00 61.93 S ATOM 4473 SG CYS A 282 42.322 48.732 15.482 1.00 64.89 S ATOM 16942 SG CYS C 146 29.762 69.730 80.614 1.00127.37 S ATOM 17130 SG CYS C 159 31.471 69.008 77.299 1.00111.13 S ATOM 17185 SG CYS C 163 32.787 71.906 79.371 1.00119.08 S ATOM 17195 SG CYS C 164 33.107 68.366 80.746 1.00108.45 S ATOM 18275 SG CYS C 233 36.504 91.333 70.828 1.00139.04 S ATOM 18300 SG CYS C 235 37.665 88.886 73.425 1.00130.85 S Time building chain proxies: 13.14, per 1000 atoms: 0.64 Number of scatterers: 20436 At special positions: 0 Unit cell: (89.04, 114.24, 124.32, 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 3 29.99 S 63 16.00 P 31 15.00 Mg 2 11.99 O 2025 8.00 N 1828 7.00 C 6433 6.00 H 10051 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: 17.49 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 164 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 235 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 233 " Number of angles added : 8 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 41.5% alpha, 13.9% beta 7 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 12.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.622A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.627A 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 235 removed outlier: 3.690A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.242A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.905A 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: 3.611A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.831A pdb=" N LEU B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 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 removed outlier: 3.619A pdb=" N THR B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.571A pdb=" N ILE B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.750A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.849A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.556A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 426 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.925A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.673A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 497 removed outlier: 3.650A pdb=" N LEU B 497 " --> pdb=" O HIS B 493 " (cutoff:3.500A) 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: 3.553A 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 Processing helix chain 'C' and resid 56 through 59 removed outlier: 3.509A pdb=" N LEU C 59 " --> pdb=" O LEU C 56 " (cutoff:3.500A) No H-bonds generated for '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 helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.247A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.297A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.297A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.666A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) 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: 7.110A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 221 through 224 removed outlier: 3.856A pdb=" N CYS C 259 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 264 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 385 through 386 removed outlier: 3.795A pdb=" N ALA C 414 " --> pdb=" O CYS C 409 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 8.14 Time building geometry restraints manager: 18.36 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: 10019 1.03 - 1.23: 44 1.23 - 1.42: 4497 1.42 - 1.62: 6061 1.62 - 1.81: 87 Bond restraints: 20708 Sorted by residual: 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 5.72e+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 4.33e+00 bond pdb=" C5' CTP F 1 " pdb=" O5' CTP F 1 " ideal model delta sigma weight residual 1.410 1.451 -0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C4 CTP F 1 " pdb=" N3 CTP F 1 " ideal model delta sigma weight residual 1.380 1.340 0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 CTP F 1 " pdb=" C5 CTP F 1 " ideal model delta sigma weight residual 1.390 1.421 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.73: 456 106.73 - 113.68: 24449 113.68 - 120.62: 7208 120.62 - 127.57: 5139 127.57 - 134.52: 145 Bond angle restraints: 37397 Sorted by residual: angle pdb=" PA CTP F 1 " pdb=" O3A CTP F 1 " pdb=" PB CTP F 1 " ideal model delta sigma weight residual 120.50 134.52 -14.02 3.00e+00 1.11e-01 2.19e+01 angle pdb=" PB CTP F 1 " pdb=" O3B CTP F 1 " pdb=" PG CTP F 1 " ideal model delta sigma weight residual 120.50 131.79 -11.29 3.00e+00 1.11e-01 1.42e+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 99.78 11.22 3.00e+00 1.11e-01 1.40e+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 99.91 11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O1B CTP F 1 " pdb=" PB CTP F 1 " pdb=" O2B CTP F 1 " ideal model delta sigma weight residual 109.50 119.32 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 37392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 9343 35.28 - 70.56: 413 70.56 - 105.84: 19 105.84 - 141.11: 1 141.11 - 176.39: 2 Dihedral angle restraints: 9778 sinusoidal: 5559 harmonic: 4219 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 320.71 166.48 154.22 1 2.00e+01 2.50e-03 4.56e+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 -169.86 -107.42 1 2.00e+01 2.50e-03 3.12e+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 -52.04 -103.46 1 2.00e+01 2.50e-03 2.96e+01 ... (remaining 9775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1440 0.051 - 0.102: 154 0.102 - 0.153: 40 0.153 - 0.204: 0 0.204 - 0.255: 1 Chirality restraints: 1635 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 -2.73 0.25 2.00e-01 2.50e+01 1.62e+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 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" C3' CTP F 1 " pdb=" C2' CTP F 1 " pdb=" C4' CTP F 1 " pdb=" O3' CTP F 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.61 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1632 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 162 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A S 8 " 0.019 2.00e-02 2.50e+03 8.45e-03 2.32e+00 pdb=" N9 A S 8 " -0.023 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 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A S 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A S 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A S 8 " 0.000 2.00e-02 2.50e+03 pdb=" H8 A S 8 " -0.000 2.00e-02 2.50e+03 pdb=" H2 A S 8 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO B 470 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.019 5.00e-02 4.00e+02 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.72: 25 1.72 - 2.44: 11247 2.44 - 3.16: 62150 3.16 - 3.88: 84118 3.88 - 4.60: 133872 Warning: very small nonbonded interaction distances. Nonbonded interactions: 291412 Sorted by model distance: nonbonded pdb=" HD2 HIS C 266 " pdb="HG13 VAL C 269 " model vdw 0.997 2.270 nonbonded pdb=" HB2 CYS C 233 " pdb="ZN ZN C 502 " model vdw 1.374 1.544 nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.484 1.850 nonbonded pdb=" O GLY A 309 " pdb="HH22 ARG B 394 " model vdw 1.559 1.850 nonbonded pdb=" OD2 ASP A 43 " pdb=" H PHE A 55 " model vdw 1.574 1.850 ... (remaining 291407 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: 1.930 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: 0.290 Extract box with map and model: 0.690 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 90.910 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 0.048 10657 Z= 0.159 Angle : 0.546 14.024 14537 Z= 0.270 Chirality : 0.037 0.255 1635 Planarity : 0.003 0.051 1766 Dihedral : 18.464 176.392 4163 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 2.43 % Allowed : 25.02 % Favored : 72.55 % 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: 1.06 (0.25), residues: 1234 helix: 1.99 (0.25), residues: 477 sheet: 0.43 (0.42), residues: 150 loop : -0.22 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 183 HIS 0.002 0.001 HIS A 371 PHE 0.010 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.005 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: B 219 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7781 (mp0) outliers start: 26 outliers final: 23 residues processed: 115 average time/residue: 0.5858 time to fit residues: 91.9073 Evaluate side-chains 112 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10657 Z= 0.282 Angle : 0.520 6.963 14537 Z= 0.268 Chirality : 0.039 0.168 1635 Planarity : 0.004 0.055 1766 Dihedral : 13.649 175.945 1829 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 3.36 % Allowed : 23.44 % Favored : 73.20 % 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: 0.89 (0.24), residues: 1234 helix: 1.79 (0.24), residues: 483 sheet: 0.29 (0.42), residues: 148 loop : -0.29 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.004 0.001 HIS C 22 PHE 0.016 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 219 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: B 222 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8151 (t70) outliers start: 36 outliers final: 23 residues processed: 117 average time/residue: 0.5711 time to fit residues: 92.1449 Evaluate side-chains 116 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10657 Z= 0.275 Angle : 0.515 6.100 14537 Z= 0.267 Chirality : 0.039 0.149 1635 Planarity : 0.004 0.055 1766 Dihedral : 13.339 173.804 1809 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 2.89 % Allowed : 23.25 % Favored : 73.86 % 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: 0.72 (0.24), residues: 1234 helix: 1.66 (0.24), residues: 484 sheet: 0.23 (0.42), residues: 148 loop : -0.40 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS C 22 PHE 0.015 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8411 (mppt) REVERT: A 148 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: B 121 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8673 (mp) REVERT: B 219 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: B 222 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8184 (t70) outliers start: 31 outliers final: 17 residues processed: 111 average time/residue: 0.6646 time to fit residues: 97.9718 Evaluate side-chains 104 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10657 Z= 0.143 Angle : 0.464 5.738 14537 Z= 0.237 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.052 1766 Dihedral : 12.982 174.752 1802 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 2.43 % Allowed : 22.88 % Favored : 74.70 % 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 (0.24), residues: 1234 helix: 1.98 (0.24), residues: 484 sheet: 0.27 (0.42), residues: 150 loop : -0.28 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.002 0.001 HIS A 367 PHE 0.010 0.001 PHE C 44 TYR 0.008 0.001 TYR A 403 ARG 0.002 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8385 (mppt) REVERT: B 216 LYS cc_start: 0.8442 (mttt) cc_final: 0.8187 (mmtt) outliers start: 26 outliers final: 19 residues processed: 112 average time/residue: 0.5921 time to fit residues: 90.0341 Evaluate side-chains 106 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10657 Z= 0.257 Angle : 0.498 5.716 14537 Z= 0.258 Chirality : 0.038 0.143 1635 Planarity : 0.004 0.054 1766 Dihedral : 12.917 174.566 1796 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.30 % Rotamer: Outliers : 3.17 % Allowed : 22.32 % Favored : 74.51 % 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: 0.84 (0.24), residues: 1234 helix: 1.80 (0.24), residues: 484 sheet: 0.24 (0.42), residues: 148 loop : -0.36 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8420 (mppt) REVERT: B 124 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.7999 (mtpp) REVERT: B 204 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: C 217 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5505 (ttt-90) outliers start: 34 outliers final: 24 residues processed: 111 average time/residue: 0.6268 time to fit residues: 93.6734 Evaluate side-chains 110 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10657 Z= 0.185 Angle : 0.473 5.746 14537 Z= 0.243 Chirality : 0.037 0.139 1635 Planarity : 0.004 0.052 1766 Dihedral : 12.869 174.914 1796 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 3.17 % Allowed : 21.85 % Favored : 74.98 % 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: 0.92 (0.24), residues: 1234 helix: 1.89 (0.24), residues: 484 sheet: 0.27 (0.42), residues: 148 loop : -0.33 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.002 0.001 HIS A 367 PHE 0.012 0.001 PHE C 44 TYR 0.010 0.001 TYR A 403 ARG 0.006 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 86 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8393 (mppt) REVERT: B 204 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: B 216 LYS cc_start: 0.8509 (mttt) cc_final: 0.8230 (mmtt) REVERT: B 222 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8154 (t70) REVERT: C 217 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.4635 (ttt-90) outliers start: 34 outliers final: 24 residues processed: 113 average time/residue: 0.6720 time to fit residues: 101.6410 Evaluate side-chains 111 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10657 Z= 0.231 Angle : 0.488 5.709 14537 Z= 0.253 Chirality : 0.038 0.137 1635 Planarity : 0.004 0.053 1766 Dihedral : 12.942 174.685 1796 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 2.99 % Allowed : 21.76 % Favored : 75.26 % 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: 0.81 (0.24), residues: 1234 helix: 1.78 (0.24), residues: 484 sheet: 0.03 (0.42), residues: 153 loop : -0.32 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8449 (mppt) REVERT: B 204 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: B 222 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8163 (t70) REVERT: B 504 ASN cc_start: 0.6851 (t0) cc_final: 0.6647 (t0) outliers start: 32 outliers final: 27 residues processed: 107 average time/residue: 0.6007 time to fit residues: 87.3706 Evaluate side-chains 111 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 81 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10657 Z= 0.195 Angle : 0.476 5.732 14537 Z= 0.245 Chirality : 0.037 0.138 1635 Planarity : 0.004 0.052 1766 Dihedral : 12.907 175.053 1796 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 3.08 % Allowed : 21.38 % Favored : 75.54 % 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 (0.24), residues: 1234 helix: 1.85 (0.24), residues: 484 sheet: 0.07 (0.42), residues: 153 loop : -0.31 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.002 0.001 HIS A 367 PHE 0.013 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.006 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8417 (mppt) REVERT: A 317 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: B 204 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: B 216 LYS cc_start: 0.8510 (mttt) cc_final: 0.8229 (mmtt) REVERT: B 222 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8165 (t70) outliers start: 33 outliers final: 28 residues processed: 111 average time/residue: 0.5991 time to fit residues: 89.4969 Evaluate side-chains 116 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 8.9990 chunk 115 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10657 Z= 0.240 Angle : 0.493 5.702 14537 Z= 0.256 Chirality : 0.038 0.137 1635 Planarity : 0.004 0.053 1766 Dihedral : 12.991 174.635 1796 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.06 % Rotamer: Outliers : 3.08 % Allowed : 21.66 % Favored : 75.26 % 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: 0.76 (0.24), residues: 1234 helix: 1.75 (0.24), residues: 484 sheet: 0.00 (0.42), residues: 153 loop : -0.36 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.006 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8454 (mppt) REVERT: A 317 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7918 (ttm170) REVERT: B 204 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: B 219 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: B 222 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8158 (t70) outliers start: 33 outliers final: 27 residues processed: 108 average time/residue: 0.6218 time to fit residues: 91.0598 Evaluate side-chains 112 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 82 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10657 Z= 0.158 Angle : 0.465 5.787 14537 Z= 0.239 Chirality : 0.036 0.139 1635 Planarity : 0.004 0.052 1766 Dihedral : 12.933 178.664 1796 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 2.80 % Allowed : 21.94 % Favored : 75.26 % 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: 0.94 (0.24), residues: 1234 helix: 1.94 (0.24), residues: 484 sheet: -0.02 (0.42), residues: 155 loop : -0.27 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.002 0.001 HIS C 191 PHE 0.011 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.005 0.000 ARG C 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8421 (mppt) REVERT: A 317 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7922 (ttm170) REVERT: B 204 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: B 216 LYS cc_start: 0.8452 (mttt) cc_final: 0.8186 (mmtt) outliers start: 30 outliers final: 27 residues processed: 111 average time/residue: 0.6138 time to fit residues: 91.8879 Evaluate side-chains 115 residues out of total 1071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102376 restraints weight = 41208.788| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.13 r_work: 0.3058 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10657 Z= 0.148 Angle : 0.458 5.822 14537 Z= 0.235 Chirality : 0.036 0.139 1635 Planarity : 0.004 0.052 1766 Dihedral : 12.648 175.153 1796 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 2.71 % Allowed : 22.13 % Favored : 75.16 % 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: 1.03 (0.24), residues: 1234 helix: 2.02 (0.24), residues: 484 sheet: 0.01 (0.42), residues: 155 loop : -0.20 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.002 0.001 HIS A 371 PHE 0.011 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.005 0.000 ARG C 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5040.56 seconds wall clock time: 88 minutes 14.50 seconds (5294.50 seconds total)