Starting phenix.real_space_refine on Sat Feb 17 06:38:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9l_29871/02_2024/8g9l_29871_trim_updated.pdb" } resolution = 3.3 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 Fe 4 7.16 5 P 30 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5670 2.51 5 N 1538 2.21 5 O 1737 1.98 5 H 8774 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 597": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17801 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 13976 Classifications: {'peptide': 868} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 822} Chain breaks: 2 Chain: "B" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3004 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain: "C" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 505 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 275 Unusual residues: {'DOC': 1, 'GTP': 1} Classifications: {'RNA': 7, 'undetermined': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 5, None: 2} Not linked: pdbres="GTP D 1 " pdbres=" G D 2 " Not linked: pdbres=" G D 8 " pdbres="DOC D 9 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" 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 15568 SG CYS B 373 72.807 34.173 28.659 1.00111.93 S ATOM 15816 SG CYS B 390 69.454 29.318 31.409 1.00119.82 S ATOM 16468 SG CYS B 430 70.198 29.608 24.975 1.00132.05 S ATOM 14227 SG CYS B 293 66.281 33.731 28.033 1.00 97.69 S Time building chain proxies: 8.85, per 1000 atoms: 0.50 Number of scatterers: 17801 At special positions: 0 Unit cell: (96.46, 106.47, 122.85, 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) Fe 4 26.01 S 46 16.00 P 30 15.00 Mg 2 11.99 O 1737 8.00 N 1538 7.00 C 5670 6.00 H 8774 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.51 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 430 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 390 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 373 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 293 " Number of angles added : 12 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 42.2% alpha, 12.7% beta 7 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 10.48 Creating SS restraints... Processing helix chain 'A' and resid 410 through 419 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 659 through 662 Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 735 through 758 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 907 through 926 Processing helix chain 'A' and resid 932 through 957 removed outlier: 4.513A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 990 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 3.926A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'A' and resid 1082 through 1095 Processing helix chain 'A' and resid 1101 through 1120 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1149 through 1159 Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1204 through 1210 Processing helix chain 'A' and resid 1212 through 1219 Processing helix chain 'A' and resid 1228 through 1235 Processing helix chain 'B' and resid 280 through 288 removed outlier: 4.128A pdb=" N GLY B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.872A pdb=" N LYS B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.798A pdb=" N ASP B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 391 through 394 No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 411 through 423 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 450 through 461 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 529 removed outlier: 4.334A pdb=" N TRP A 498 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 390 Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 6.208A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A 549 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN A 555 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 849 through 851 removed outlier: 7.056A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1001 through 1005 removed outlier: 3.856A pdb=" N GLY A1038 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP A 859 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE A1036 " --> pdb=" O ASP A 859 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1133 363 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 16.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 8757 1.13 - 1.42: 3789 1.42 - 1.70: 5429 1.70 - 1.99: 63 1.99 - 2.28: 12 Bond restraints: 18050 Sorted by residual: bond pdb=" C2' DGT A1501 " pdb=" C3' DGT A1501 " ideal model delta sigma weight residual 1.284 1.541 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C4' DOC D 9 " pdb=" C3' DOC D 9 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4' DGT A1501 " pdb=" O4' DGT A1501 " ideal model delta sigma weight residual 1.272 1.449 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" O4' DOC D 9 " pdb=" C1' DOC D 9 " ideal model delta sigma weight residual 1.268 1.438 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" C4 DGT A1501 " pdb=" N3 DGT A1501 " ideal model delta sigma weight residual 1.502 1.335 0.167 2.00e-02 2.50e+03 7.01e+01 ... (remaining 18045 not shown) Histogram of bond angle deviations from ideal: 73.66 - 85.80: 12 85.80 - 97.95: 0 97.95 - 110.10: 16829 110.10 - 122.25: 13116 122.25 - 134.39: 2739 Bond angle restraints: 32696 Sorted by residual: angle pdb=" PA GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sigma weight residual 120.50 133.09 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" PB GTP D 1 " pdb=" O3B GTP D 1 " pdb=" PG GTP D 1 " ideal model delta sigma weight residual 120.50 131.93 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" OP1 DOC D 9 " pdb=" P DOC D 9 " pdb=" OP2 DOC D 9 " ideal model delta sigma weight residual 109.57 119.82 -10.25 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N GLY A1018 " pdb=" CA GLY A1018 " pdb=" C GLY A1018 " ideal model delta sigma weight residual 113.18 105.17 8.01 2.37e+00 1.78e-01 1.14e+01 angle pdb=" C2' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" C4' GTP D 1 " ideal model delta sigma weight residual 111.00 100.91 10.09 3.00e+00 1.11e-01 1.13e+01 ... (remaining 32691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 7993 33.47 - 66.93: 388 66.93 - 100.40: 21 100.40 - 133.87: 3 133.87 - 167.33: 3 Dihedral angle restraints: 8408 sinusoidal: 4763 harmonic: 3645 Sorted by residual: dihedral pdb=" C5' GTP D 1 " pdb=" O5' GTP D 1 " pdb=" PA GTP D 1 " pdb=" O3A GTP D 1 " ideal model delta sinusoidal sigma weight residual 69.27 -98.06 167.33 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3B GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PB GTP D 1 " pdb=" PA GTP D 1 " ideal model delta sinusoidal sigma weight residual -68.92 79.51 -148.43 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" O5' GTP D 1 " pdb=" O3A GTP D 1 " pdb=" PA GTP D 1 " pdb=" PB GTP D 1 " ideal model delta sinusoidal sigma weight residual 274.12 127.92 146.20 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 8405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1270 0.070 - 0.141: 131 0.141 - 0.211: 5 0.211 - 0.281: 1 0.281 - 0.351: 2 Chirality restraints: 1409 Sorted by residual: chirality pdb=" C3' DGT A1501 " pdb=" C2' DGT A1501 " pdb=" C4' DGT A1501 " pdb=" O3' DGT A1501 " both_signs ideal model delta sigma weight residual False -2.42 -2.78 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C2' GTP D 1 " pdb=" C1' GTP D 1 " pdb=" C3' GTP D 1 " pdb=" O2' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' GTP D 1 " pdb=" C2' GTP D 1 " pdb=" C4' GTP D 1 " pdb=" O3' GTP D 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1406 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1018 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C GLY A1018 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A1018 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A1019 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 6 " 0.025 2.00e-02 2.50e+03 1.11e-02 3.40e+00 pdb=" N1 C D 6 " -0.026 2.00e-02 2.50e+03 pdb=" C2 C D 6 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C D 6 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C D 6 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C D 6 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C D 6 " -0.003 2.00e-02 2.50e+03 pdb=" H5 C D 6 " 0.002 2.00e-02 2.50e+03 pdb=" H6 C D 6 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 5 " -0.020 2.00e-02 2.50e+03 8.12e-03 2.14e+00 pdb=" N9 A D 5 " 0.020 2.00e-02 2.50e+03 pdb=" C8 A D 5 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A D 5 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A D 5 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A D 5 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A D 5 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A D 5 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 5 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A D 5 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A D 5 " 0.002 2.00e-02 2.50e+03 pdb=" H8 A D 5 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A D 5 " 0.001 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1249 2.21 - 2.81: 36829 2.81 - 3.41: 46904 3.41 - 4.00: 62835 4.00 - 4.60: 96676 Nonbonded interactions: 244493 Sorted by model distance: nonbonded pdb=" O GLN A 397 " pdb=" HG1 THR A 400 " model vdw 1.613 1.850 nonbonded pdb=" HG SER A 375 " pdb=" OD2 ASP A 630 " model vdw 1.644 1.850 nonbonded pdb=" OE2 GLU A 416 " pdb=" H GLU A 471 " model vdw 1.662 1.850 nonbonded pdb="HH12 ARG A 667 " pdb=" O ASN A 683 " model vdw 1.665 1.850 nonbonded pdb=" O SER A 862 " pdb=" HG SER A 866 " model vdw 1.666 1.850 ... (remaining 244488 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=1.00 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: 1.720 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: 10.290 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 75.470 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.008 0.257 9276 Z= 0.419 Angle : 0.567 12.595 12672 Z= 0.293 Chirality : 0.043 0.351 1409 Planarity : 0.004 0.036 1527 Dihedral : 19.148 167.334 3571 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 18.15 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.08 (0.27), residues: 1046 helix: 0.32 (0.24), residues: 472 sheet: 0.54 (0.43), residues: 145 loop : -0.25 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 498 HIS 0.003 0.001 HIS A1152 PHE 0.012 0.001 PHE A 583 TYR 0.007 0.001 TYR A 425 ARG 0.003 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.6070 time to fit residues: 101.4607 Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 549 ASN A 714 GLN A1009 ASN A1109 GLN A1241 GLN B 458 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9276 Z= 0.307 Angle : 0.552 8.411 12672 Z= 0.279 Chirality : 0.040 0.144 1409 Planarity : 0.004 0.080 1527 Dihedral : 15.800 160.834 1447 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.96 % Allowed : 19.21 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.83 (0.27), residues: 1046 helix: 1.34 (0.24), residues: 474 sheet: 0.62 (0.42), residues: 150 loop : -0.30 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.003 0.001 HIS B 309 PHE 0.008 0.001 PHE A 583 TYR 0.010 0.001 TYR A 425 ARG 0.008 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 0.4474 time to fit residues: 45.9048 Evaluate side-chains 64 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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: 0.8428 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9276 Z= 0.225 Angle : 0.503 7.769 12672 Z= 0.256 Chirality : 0.039 0.145 1409 Planarity : 0.003 0.041 1527 Dihedral : 15.079 145.697 1447 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.96 % Allowed : 18.05 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1046 helix: 1.81 (0.24), residues: 472 sheet: 0.65 (0.42), residues: 149 loop : -0.22 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.002 0.000 HIS B 394 PHE 0.008 0.001 PHE A 583 TYR 0.009 0.001 TYR A 953 ARG 0.008 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 GLU cc_start: 0.8383 (mp0) cc_final: 0.8099 (mp0) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.4385 time to fit residues: 44.0284 Evaluate side-chains 67 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9276 Z= 0.211 Angle : 0.494 7.274 12672 Z= 0.249 Chirality : 0.039 0.143 1409 Planarity : 0.003 0.033 1527 Dihedral : 14.556 167.428 1447 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.49 % Allowed : 17.94 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.46 (0.27), residues: 1046 helix: 2.04 (0.24), residues: 474 sheet: 0.72 (0.42), residues: 149 loop : -0.13 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1156 HIS 0.002 0.000 HIS B 394 PHE 0.008 0.001 PHE A 583 TYR 0.010 0.001 TYR A 953 ARG 0.004 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 GLU cc_start: 0.8423 (mp0) cc_final: 0.8126 (mp0) outliers start: 14 outliers final: 7 residues processed: 73 average time/residue: 0.4550 time to fit residues: 48.0254 Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9276 Z= 0.338 Angle : 0.534 7.506 12672 Z= 0.275 Chirality : 0.040 0.144 1409 Planarity : 0.003 0.028 1527 Dihedral : 14.181 142.509 1447 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.27 % Allowed : 18.26 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1046 helix: 1.80 (0.24), residues: 476 sheet: 0.71 (0.43), residues: 149 loop : -0.21 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1156 HIS 0.002 0.001 HIS A 553 PHE 0.007 0.001 PHE B 318 TYR 0.010 0.001 TYR A 953 ARG 0.002 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 GLU cc_start: 0.8444 (mp0) cc_final: 0.8147 (mp0) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.4286 time to fit residues: 44.6816 Evaluate side-chains 63 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9276 Z= 0.261 Angle : 0.519 7.275 12672 Z= 0.263 Chirality : 0.040 0.163 1409 Planarity : 0.003 0.027 1527 Dihedral : 13.554 110.857 1447 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.85 % Allowed : 19.00 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.37 (0.27), residues: 1046 helix: 1.93 (0.24), residues: 476 sheet: 0.72 (0.42), residues: 149 loop : -0.16 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1156 HIS 0.002 0.001 HIS A 566 PHE 0.007 0.001 PHE A 583 TYR 0.009 0.001 TYR A 425 ARG 0.006 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 GLU cc_start: 0.8443 (mp0) cc_final: 0.8146 (mp0) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.4241 time to fit residues: 40.4496 Evaluate side-chains 63 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8491 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9276 Z= 0.281 Angle : 0.526 7.901 12672 Z= 0.267 Chirality : 0.040 0.141 1409 Planarity : 0.003 0.028 1527 Dihedral : 13.384 104.781 1447 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.17 % Allowed : 18.37 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1046 helix: 1.93 (0.24), residues: 477 sheet: 0.67 (0.43), residues: 149 loop : -0.18 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.002 0.001 HIS B 388 PHE 0.007 0.001 PHE B 337 TYR 0.010 0.001 TYR A 953 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 GLU cc_start: 0.8461 (mp0) cc_final: 0.8156 (mp0) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.4172 time to fit residues: 42.0945 Evaluate side-chains 64 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9276 Z= 0.214 Angle : 0.506 7.848 12672 Z= 0.257 Chirality : 0.039 0.141 1409 Planarity : 0.003 0.026 1527 Dihedral : 13.269 102.887 1447 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.85 % Allowed : 18.90 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1046 helix: 2.09 (0.24), residues: 477 sheet: 0.79 (0.43), residues: 148 loop : -0.13 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1156 HIS 0.002 0.000 HIS A 566 PHE 0.007 0.001 PHE A 583 TYR 0.009 0.001 TYR A 953 ARG 0.002 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.8882 (mmt) cc_final: 0.8629 (mmt) REVERT: B 345 GLU cc_start: 0.8457 (mp0) cc_final: 0.8160 (mp0) outliers start: 8 outliers final: 7 residues processed: 66 average time/residue: 0.4277 time to fit residues: 41.6537 Evaluate side-chains 63 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9276 Z= 0.188 Angle : 0.500 8.951 12672 Z= 0.253 Chirality : 0.039 0.141 1409 Planarity : 0.003 0.027 1527 Dihedral : 13.144 100.571 1447 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.85 % Allowed : 18.47 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.66 (0.27), residues: 1046 helix: 2.18 (0.24), residues: 478 sheet: 0.86 (0.44), residues: 148 loop : -0.02 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1156 HIS 0.002 0.000 HIS A 566 PHE 0.007 0.001 PHE A 583 TYR 0.009 0.001 TYR A 953 ARG 0.002 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.8872 (mmt) cc_final: 0.8623 (mmt) REVERT: B 345 GLU cc_start: 0.8449 (mp0) cc_final: 0.8150 (mp0) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.4869 time to fit residues: 45.6785 Evaluate side-chains 65 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9276 Z= 0.232 Angle : 0.501 7.925 12672 Z= 0.257 Chirality : 0.039 0.141 1409 Planarity : 0.003 0.027 1527 Dihedral : 13.054 97.505 1447 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.96 % Allowed : 18.15 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.64 (0.27), residues: 1046 helix: 2.16 (0.24), residues: 478 sheet: 0.89 (0.44), residues: 148 loop : -0.05 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1156 HIS 0.002 0.001 HIS A 982 PHE 0.006 0.001 PHE A 583 TYR 0.009 0.001 TYR A 953 ARG 0.002 0.000 ARG B 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.8903 (mmt) cc_final: 0.8666 (mmt) REVERT: B 345 GLU cc_start: 0.8467 (mp0) cc_final: 0.8168 (mp0) outliers start: 9 outliers final: 8 residues processed: 66 average time/residue: 0.4233 time to fit residues: 41.2632 Evaluate side-chains 65 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain B residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 = 0.3110 r_free = 0.3110 target = 0.049157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.036445 restraints weight = 113453.334| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 4.17 r_work: 0.2553 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9276 Z= 0.159 Angle : 0.491 8.598 12672 Z= 0.248 Chirality : 0.039 0.140 1409 Planarity : 0.003 0.027 1527 Dihedral : 12.907 96.260 1447 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.85 % Allowed : 18.37 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.88 (0.28), residues: 1046 helix: 2.36 (0.25), residues: 478 sheet: 0.95 (0.44), residues: 148 loop : 0.10 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1156 HIS 0.002 0.000 HIS A 566 PHE 0.008 0.001 PHE A 583 TYR 0.010 0.001 TYR A 935 ARG 0.002 0.000 ARG B 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3911.53 seconds wall clock time: 70 minutes 16.34 seconds (4216.34 seconds total)