Starting phenix.real_space_refine on Fri Sep 11 14:11:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.map" model { file = "/net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d96_27256/09_2026/8d96_27256.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 35 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 5782 2.51 5 N 1567 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9203 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1525 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "C" Number of atoms: 6988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6988 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 825} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'GTP': 1} Classifications: {'DNA': 3, 'RNAv2': 8, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9, None: 1} Not linked: pdbres="GTP E 1 " pdbres=" G E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 810 SG CYS B 367 70.443 91.366 103.166 1.00166.89 S ATOM 938 SG CYS B 384 64.388 91.569 104.702 1.00238.63 S ATOM 1254 SG CYS B 424 69.032 91.059 109.234 1.00264.10 S ATOM 139 SG CYS B 287 67.225 85.996 105.788 1.00209.78 S Time building chain proxies: 2.18, per 1000 atoms: 0.24 Number of scatterers: 9203 At special positions: 0 Unit cell: (95.2, 112, 132.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 55 16.00 P 35 15.00 Mg 1 11.99 O 1759 8.00 N 1567 7.00 C 5782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 245.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 424 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 367 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 384 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 287 " 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: 2004 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 50.1% alpha, 16.2% beta 2 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 285 through 299 Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.523A pdb=" N GLY B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.929A pdb=" N GLN B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 443 through 456 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 597 through 606 Processing helix chain 'C' and resid 614 through 630 Processing helix chain 'C' and resid 642 through 655 Processing helix chain 'C' and resid 658 through 663 removed outlier: 3.512A pdb=" N ILE C 662 " --> pdb=" O TRP C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 Processing helix chain 'C' and resid 693 through 701 Processing helix chain 'C' and resid 707 through 716 Processing helix chain 'C' and resid 725 through 733 removed outlier: 3.691A pdb=" N GLN C 729 " --> pdb=" O GLU C 726 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 733 " --> pdb=" O ASN C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 760 Processing helix chain 'C' and resid 760 through 773 removed outlier: 3.586A pdb=" N LEU C 764 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 Processing helix chain 'C' and resid 784 through 799 Processing helix chain 'C' and resid 863 through 873 Processing helix chain 'C' and resid 909 through 931 removed outlier: 4.006A pdb=" N LYS C 917 " --> pdb=" O ARG C 913 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 918 " --> pdb=" O GLU C 914 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 960 removed outlier: 3.696A pdb=" N MET C 956 " --> pdb=" O THR C 952 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR C 957 " --> pdb=" O ALA C 953 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 958 " --> pdb=" O ASN C 954 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 960 " --> pdb=" O MET C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 993 removed outlier: 3.857A pdb=" N ALA C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1033 removed outlier: 3.513A pdb=" N VAL C1018 " --> pdb=" O ASN C1014 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR C1033 " --> pdb=" O VAL C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1081 Processing helix chain 'C' and resid 1085 through 1101 Processing helix chain 'C' and resid 1104 through 1126 removed outlier: 3.537A pdb=" N ILE C1108 " --> pdb=" O SER C1104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C1109 " --> pdb=" O ARG C1105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C1110 " --> pdb=" O ASP C1106 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1134 removed outlier: 3.879A pdb=" N GLU C1134 " --> pdb=" O SER C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.784A pdb=" N TYR C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1152 through 1165 Processing helix chain 'C' and resid 1187 through 1190 Processing helix chain 'C' and resid 1194 through 1201 removed outlier: 3.556A pdb=" N LEU C1198 " --> pdb=" O ALA C1194 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN C1199 " --> pdb=" O PRO C1195 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS C1200 " --> pdb=" O GLU C1196 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C1201 " --> pdb=" O GLN C1197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1194 through 1201' Processing helix chain 'C' and resid 1207 through 1215 removed outlier: 3.535A pdb=" N TYR C1211 " --> pdb=" O ASP C1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1224 removed outlier: 4.264A pdb=" N VAL C1219 " --> pdb=" O GLN C1215 " (cutoff:3.500A) Processing helix chain 'C' and resid 1231 through 1240 Processing sheet with id=AA1, first strand: chain 'C' and resid 516 through 520 removed outlier: 9.929A pdb=" N VAL C 516 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER C 375 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ALA C 518 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS C 377 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA C 520 " --> pdb=" O CYS C 377 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET C 379 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 372 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 367 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL C 358 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU C 350 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE C 360 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA C 348 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C 362 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP C 366 " --> pdb=" O HIS C 342 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS C 342 " --> pdb=" O TRP C 366 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 341 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP C 498 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 431 through 438 removed outlier: 3.508A pdb=" N SER C 450 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLU C 451 " --> pdb=" O PRO C 391 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS C 475 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 609 through 612 removed outlier: 9.006A pdb=" N GLU C 610 " --> pdb=" O HIS C 582 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS C 584 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA C 612 " --> pdb=" O CYS C 584 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL C 586 " --> pdb=" O ALA C 612 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE C 558 " --> pdb=" O SER C 587 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 558 " --> pdb=" O MET C 547 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N MET C 547 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N MET C 560 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LYS C 545 " --> pdb=" O MET C 560 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA C 562 " --> pdb=" O SER C 543 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER C 543 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL C 564 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA C 541 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N HIS C 566 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 539 " --> pdb=" O HIS C 566 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 542 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE C 634 " --> pdb=" O CYS C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 850 through 852 removed outlier: 3.558A pdb=" N GLY C 850 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE C1044 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C1060 " --> pdb=" O PHE C1044 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS C1054 " --> pdb=" O LEU C1050 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN C1067 " --> pdb=" O THR C1063 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 997 through 1000 removed outlier: 4.488A pdb=" N GLU C 997 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET C1007 " --> pdb=" O ILE C 999 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C1008 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1135 through 1138 Processing sheet with id=AA7, first strand: chain 'C' and resid 1135 through 1138 removed outlier: 3.686A pdb=" N THR C1205 " --> pdb=" O GLN C1181 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 3975 1.43 - 1.64: 5404 1.64 - 1.86: 80 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 9471 Sorted by residual: bond pdb=" C3' DC F 16 " pdb=" C2' DC F 16 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG F 12 " pdb=" C2' DG F 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.41e+00 bond pdb=" C3' DC F 17 " pdb=" C2' DC F 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.33e+00 bond pdb=" C2 GTP E 1 " pdb=" N3 GTP E 1 " ideal model delta sigma weight residual 1.380 1.329 0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" C3' DT F 11 " pdb=" C2' DT F 11 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.73e+00 ... (remaining 9466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 12740 2.08 - 4.15: 164 4.15 - 6.23: 26 6.23 - 8.31: 6 8.31 - 10.39: 6 Bond angle restraints: 12942 Sorted by residual: angle pdb=" N3 DT F 20 " pdb=" C4 DT F 20 " pdb=" O4 DT F 20 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT F 11 " pdb=" C4 DT F 11 " pdb=" O4 DT F 11 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT F 5 " pdb=" C4 DT F 5 " pdb=" O4 DT F 5 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT F 8 " pdb=" C4 DT F 8 " pdb=" O4 DT F 8 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" O4 DT F 8 " pdb=" C4 DT F 8 " pdb=" C5 DT F 8 " ideal model delta sigma weight residual 124.90 122.32 2.58 7.00e-01 2.04e+00 1.35e+01 ... (remaining 12937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 5349 31.27 - 62.53: 278 62.53 - 93.80: 27 93.80 - 125.06: 1 125.06 - 156.33: 3 Dihedral angle restraints: 5658 sinusoidal: 2561 harmonic: 3097 Sorted by residual: dihedral pdb=" C4' G E 9 " pdb=" C3' G E 9 " pdb=" C2' G E 9 " pdb=" C1' G E 9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.28 72.62 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" O4' G E 9 " pdb=" C4' G E 9 " pdb=" C3' G E 9 " pdb=" C2' G E 9 " ideal model delta sinusoidal sigma weight residual -35.15 23.24 -58.38 1 4.00e+00 6.25e-02 2.85e+02 dihedral pdb=" O4' G E 9 " pdb=" C2' G E 9 " pdb=" C1' G E 9 " pdb=" C3' G E 9 " ideal model delta sinusoidal sigma weight residual -94.41 -37.91 -56.50 3 3.80e+00 6.93e-02 1.46e+02 ... (remaining 5655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1417 0.120 - 0.239: 16 0.239 - 0.359: 2 0.359 - 0.479: 0 0.479 - 0.598: 1 Chirality restraints: 1436 Sorted by residual: chirality pdb=" P G E 2 " pdb=" OP1 G E 2 " pdb=" OP2 G E 2 " pdb=" O5' G E 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.77 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" C2' G E 9 " pdb=" C3' G E 9 " pdb=" O2' G E 9 " pdb=" C1' G E 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' G E 9 " pdb=" C4' G E 9 " pdb=" O3' G E 9 " pdb=" C2' G E 9 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1433 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 642 " 0.007 2.00e-02 2.50e+03 7.37e-03 9.50e-01 pdb=" CG PHE C 642 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE C 642 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 642 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 642 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 642 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 642 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 443 " 0.016 5.00e-02 4.00e+02 2.41e-02 9.26e-01 pdb=" N PRO B 444 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 444 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 444 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 303 " 0.006 2.00e-02 2.50e+03 7.85e-03 9.24e-01 pdb=" CG HIS B 303 " -0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS B 303 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS B 303 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 303 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 303 " -0.000 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 24 2.45 - 3.06: 5654 3.06 - 3.67: 13543 3.67 - 4.29: 18869 4.29 - 4.90: 31991 Nonbonded interactions: 70081 Sorted by model distance: nonbonded pdb=" O ASP B 361 " pdb=" C2 DA F 19 " model vdw 1.836 3.340 nonbonded pdb=" OH TYR B 362 " pdb=" OP2 DA F 18 " model vdw 1.844 3.040 nonbonded pdb=" OD1 ASN B 348 " pdb=" N4 DC F 17 " model vdw 1.845 3.120 nonbonded pdb=" NE2 HIS B 300 " pdb=" O2G GTP E 1 " model vdw 2.005 3.120 nonbonded pdb=" CE1 HIS B 300 " pdb=" O2G GTP E 1 " model vdw 2.009 2.608 ... (remaining 70076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.220 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.570 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.005 0.357 9477 Z= 0.420 Angle : 0.631 10.386 12954 Z= 0.356 Chirality : 0.047 0.598 1436 Planarity : 0.002 0.024 1533 Dihedral : 17.432 156.329 3654 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 0.11 % Allowed : 12.20 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.28), residues: 1046 helix: 2.36 (0.25), residues: 476 sheet: 0.67 (0.45), residues: 150 loop : 0.47 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 296 TYR 0.014 0.001 TYR C 596 PHE 0.017 0.001 PHE C 642 TRP 0.003 0.001 TRP C1160 HIS 0.010 0.001 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.20 ( 9471) covalent geometry : angle 0.61578 / 0.36 (12942) hydrogen bonds : bond 0.18749 / 13.46 ( 416) hydrogen bonds : angle 6.02799 / 4.21 ( 1198) metal coordination : bond 0.00235 / 0.12 ( 4) metal coordination : angle 4.49527 / 2.09 ( 12) Misc. bond : bond 0.25439 / 13.37 ( 2) *********************** 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 50 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.356 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.1214 time to fit residues: 8.2142 Evaluate side-chains 39 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041105 restraints weight = 37956.920| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.91 r_work: 0.2685 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9477 Z= 0.191 Angle : 0.647 14.945 12954 Z= 0.322 Chirality : 0.051 0.950 1436 Planarity : 0.004 0.070 1533 Dihedral : 14.455 171.162 1476 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.96 % Favored : 96.85 % Rotamer: Outliers : 1.68 % Allowed : 12.41 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.28), residues: 1046 helix: 2.31 (0.24), residues: 474 sheet: 0.70 (0.44), residues: 152 loop : 0.41 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 453 TYR 0.015 0.001 TYR B 347 PHE 0.016 0.001 PHE C 341 TRP 0.005 0.001 TRP C 659 HIS 0.015 0.002 HIS C1250 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 9471) covalent geometry : angle 0.63213 / 0.32 (12942) hydrogen bonds : bond 0.04379 / 3.09 ( 416) hydrogen bonds : angle 4.73053 / 3.34 ( 1198) metal coordination : bond 0.00775 / 0.38 ( 4) metal coordination : angle 4.51279 / 2.09 ( 12) Misc. bond : bond 0.00554 / 0.27 ( 2) *********************** 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 58 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 553 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.7941 (t70) outliers start: 16 outliers final: 7 residues processed: 55 average time/residue: 0.1006 time to fit residues: 7.9832 Evaluate side-chains 48 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 0.0570 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.041814 restraints weight = 37699.267| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.95 r_work: 0.2682 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9477 Z= 0.107 Angle : 0.519 9.035 12954 Z= 0.266 Chirality : 0.042 0.262 1436 Planarity : 0.003 0.029 1533 Dihedral : 14.277 170.144 1476 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 1.68 % Allowed : 12.72 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.28), residues: 1046 helix: 2.33 (0.24), residues: 466 sheet: 1.05 (0.47), residues: 137 loop : 0.42 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 453 TYR 0.007 0.001 TYR B 347 PHE 0.020 0.001 PHE C 642 TRP 0.005 0.001 TRP C1160 HIS 0.005 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 9471) covalent geometry : angle 0.50113 / 0.27 (12942) hydrogen bonds : bond 0.03732 / 2.68 ( 416) hydrogen bonds : angle 4.41880 / 3.11 ( 1198) metal coordination : bond 0.00444 / 0.22 ( 4) metal coordination : angle 4.47412 / 2.17 ( 12) Misc. bond : bond 0.00164 / 0.08 ( 2) *********************** 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 58 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.368 Fit side-chains REVERT: C 553 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.7977 (t70) REVERT: C 686 CYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8659 (p) outliers start: 16 outliers final: 6 residues processed: 54 average time/residue: 0.1001 time to fit residues: 7.9488 Evaluate side-chains 48 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.060654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.040666 restraints weight = 38213.218| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.80 r_work: 0.2673 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9477 Z= 0.181 Angle : 0.559 9.523 12954 Z= 0.283 Chirality : 0.043 0.222 1436 Planarity : 0.003 0.029 1533 Dihedral : 13.852 150.706 1476 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.96 % Favored : 96.85 % Rotamer: Outliers : 2.10 % Allowed : 12.83 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.28), residues: 1046 helix: 2.25 (0.24), residues: 473 sheet: 0.60 (0.44), residues: 153 loop : 0.27 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 682 TYR 0.010 0.001 TYR C 452 PHE 0.017 0.001 PHE C 642 TRP 0.005 0.001 TRP C1160 HIS 0.004 0.001 HIS C1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 9471) covalent geometry : angle 0.53907 / 0.28 (12942) hydrogen bonds : bond 0.03957 / 2.77 ( 416) hydrogen bonds : angle 4.34203 / 3.07 ( 1198) metal coordination : bond 0.00584 / 0.29 ( 4) metal coordination : angle 4.83411 / 2.33 ( 12) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** 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 60 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 553 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.7937 (t70) REVERT: C 686 CYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8671 (p) REVERT: C 990 MET cc_start: 0.8873 (tmm) cc_final: 0.8655 (tmm) outliers start: 20 outliers final: 12 residues processed: 57 average time/residue: 0.0930 time to fit residues: 7.8452 Evaluate side-chains 54 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.060841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040736 restraints weight = 38296.161| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.97 r_work: 0.2661 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9477 Z= 0.144 Angle : 0.538 9.427 12954 Z= 0.273 Chirality : 0.042 0.185 1436 Planarity : 0.003 0.032 1533 Dihedral : 13.613 135.013 1476 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 2.00 % Allowed : 13.46 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.27), residues: 1046 helix: 2.31 (0.24), residues: 472 sheet: 0.79 (0.47), residues: 137 loop : 0.27 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 682 TYR 0.007 0.001 TYR C 732 PHE 0.013 0.001 PHE C 642 TRP 0.005 0.001 TRP C1160 HIS 0.003 0.001 HIS C1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9471) covalent geometry : angle 0.51518 / 0.27 (12942) hydrogen bonds : bond 0.03745 / 2.63 ( 416) hydrogen bonds : angle 4.27499 / 3.03 ( 1198) metal coordination : bond 0.00448 / 0.22 ( 4) metal coordination : angle 5.14623 / 2.60 ( 12) Misc. bond : bond 0.00050 / 0.03 ( 2) *********************** 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 59 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 686 CYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8665 (p) REVERT: C 990 MET cc_start: 0.8949 (tmm) cc_final: 0.8680 (tmm) outliers start: 19 outliers final: 12 residues processed: 54 average time/residue: 0.0855 time to fit residues: 6.8570 Evaluate side-chains 53 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.061244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041285 restraints weight = 37988.828| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.87 r_work: 0.2689 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9477 Z= 0.111 Angle : 0.519 9.703 12954 Z= 0.264 Chirality : 0.041 0.166 1436 Planarity : 0.003 0.032 1533 Dihedral : 13.232 107.140 1476 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.29 % Favored : 97.51 % Rotamer: Outliers : 1.79 % Allowed : 13.35 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.28), residues: 1046 helix: 2.45 (0.24), residues: 466 sheet: 0.87 (0.46), residues: 138 loop : 0.37 (0.33), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 682 TYR 0.008 0.001 TYR C 732 PHE 0.014 0.001 PHE C 642 TRP 0.005 0.001 TRP C1160 HIS 0.002 0.000 HIS C1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9471) covalent geometry : angle 0.49379 / 0.26 (12942) hydrogen bonds : bond 0.03399 / 2.39 ( 416) hydrogen bonds : angle 4.19498 / 2.97 ( 1198) metal coordination : bond 0.00297 / 0.15 ( 4) metal coordination : angle 5.26402 / 2.72 ( 12) Misc. bond : bond 0.00048 / 0.03 ( 2) *********************** 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 58 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 553 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.7958 (t70) REVERT: C 686 CYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8645 (p) REVERT: C 990 MET cc_start: 0.8876 (tmm) cc_final: 0.8633 (tmm) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.1010 time to fit residues: 8.1635 Evaluate side-chains 55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.060208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.039961 restraints weight = 38405.990| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.92 r_work: 0.2650 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9477 Z= 0.177 Angle : 0.570 11.008 12954 Z= 0.286 Chirality : 0.042 0.168 1436 Planarity : 0.003 0.035 1533 Dihedral : 13.054 103.206 1476 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.68 % Favored : 97.13 % Rotamer: Outliers : 1.68 % Allowed : 13.77 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.28), residues: 1046 helix: 2.35 (0.25), residues: 473 sheet: 0.76 (0.46), residues: 137 loop : 0.23 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1081 TYR 0.009 0.001 TYR C 452 PHE 0.012 0.001 PHE B 447 TRP 0.006 0.001 TRP C1160 HIS 0.003 0.001 HIS C1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 9471) covalent geometry : angle 0.54325 / 0.29 (12942) hydrogen bonds : bond 0.03936 / 2.75 ( 416) hydrogen bonds : angle 4.23689 / 3.01 ( 1198) metal coordination : bond 0.00558 / 0.28 ( 4) metal coordination : angle 5.64575 / 2.89 ( 12) Misc. bond : bond 0.00092 / 0.05 ( 2) *********************** 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 56 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 384 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8633 (mt-10) REVERT: C 553 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.7968 (t70) REVERT: C 686 CYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 990 MET cc_start: 0.8901 (tmm) cc_final: 0.8638 (tmm) outliers start: 16 outliers final: 12 residues processed: 54 average time/residue: 0.0887 time to fit residues: 6.8720 Evaluate side-chains 55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.041202 restraints weight = 37787.507| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.85 r_work: 0.2656 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9477 Z= 0.107 Angle : 0.530 11.017 12954 Z= 0.267 Chirality : 0.041 0.165 1436 Planarity : 0.003 0.035 1533 Dihedral : 13.030 102.529 1476 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 13.56 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.28), residues: 1046 helix: 2.52 (0.25), residues: 466 sheet: 0.84 (0.46), residues: 137 loop : 0.39 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1167 TYR 0.008 0.001 TYR C 732 PHE 0.011 0.001 PHE B 447 TRP 0.005 0.001 TRP C 746 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 9471) covalent geometry : angle 0.50027 / 0.27 (12942) hydrogen bonds : bond 0.03397 / 2.39 ( 416) hydrogen bonds : angle 4.14010 / 2.93 ( 1198) metal coordination : bond 0.00375 / 0.19 ( 4) metal coordination : angle 5.76865 / 3.07 ( 12) Misc. bond : bond 0.00051 / 0.03 ( 2) *********************** 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 58 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 384 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8565 (mt-10) REVERT: C 553 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.7946 (t70) REVERT: C 686 CYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 990 MET cc_start: 0.8848 (tmm) cc_final: 0.8608 (tmm) outliers start: 18 outliers final: 12 residues processed: 56 average time/residue: 0.1000 time to fit residues: 8.2770 Evaluate side-chains 55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.0020 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 0.0070 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.061254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.041370 restraints weight = 37856.012| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.85 r_work: 0.2695 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9477 Z= 0.107 Angle : 0.533 11.434 12954 Z= 0.268 Chirality : 0.041 0.164 1436 Planarity : 0.003 0.035 1533 Dihedral : 13.038 102.305 1476 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.61 % Rotamer: Outliers : 1.68 % Allowed : 13.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.28), residues: 1046 helix: 2.56 (0.24), residues: 466 sheet: 0.89 (0.46), residues: 137 loop : 0.40 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 682 TYR 0.008 0.001 TYR B 427 PHE 0.027 0.001 PHE B 428 TRP 0.005 0.001 TRP C1160 HIS 0.006 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 9471) covalent geometry : angle 0.50308 / 0.27 (12942) hydrogen bonds : bond 0.03346 / 2.32 ( 416) hydrogen bonds : angle 4.08435 / 2.88 ( 1198) metal coordination : bond 0.00329 / 0.16 ( 4) metal coordination : angle 5.82625 / 3.09 ( 12) Misc. bond : bond 0.00066 / 0.03 ( 2) *********************** 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 56 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 384 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8571 (mt-10) REVERT: C 553 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.7968 (t70) REVERT: C 686 CYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8542 (p) REVERT: C 990 MET cc_start: 0.8875 (tmm) cc_final: 0.8619 (tmm) outliers start: 16 outliers final: 12 residues processed: 54 average time/residue: 0.0983 time to fit residues: 7.6879 Evaluate side-chains 54 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.0020 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.060807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.040781 restraints weight = 37889.621| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.88 r_work: 0.2671 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9477 Z= 0.138 Angle : 0.553 12.252 12954 Z= 0.275 Chirality : 0.042 0.163 1436 Planarity : 0.003 0.035 1533 Dihedral : 13.069 101.419 1476 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 1.58 % Allowed : 13.77 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.28), residues: 1046 helix: 2.44 (0.25), residues: 473 sheet: 0.74 (0.43), residues: 154 loop : 0.36 (0.34), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 784 TYR 0.007 0.001 TYR C 452 PHE 0.011 0.001 PHE B 447 TRP 0.006 0.001 TRP C1160 HIS 0.003 0.001 HIS C1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9471) covalent geometry : angle 0.52230 / 0.27 (12942) hydrogen bonds : bond 0.03556 / 2.48 ( 416) hydrogen bonds : angle 4.10465 / 2.90 ( 1198) metal coordination : bond 0.00517 / 0.26 ( 4) metal coordination : angle 6.02792 / 3.17 ( 12) Misc. bond : bond 0.00076 / 0.04 ( 2) ********************** 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 54 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 384 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8597 (mt-10) REVERT: C 553 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.7933 (t70) REVERT: C 686 CYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8584 (p) REVERT: C 990 MET cc_start: 0.8861 (tmm) cc_final: 0.8616 (tmm) outliers start: 15 outliers final: 12 residues processed: 52 average time/residue: 0.0930 time to fit residues: 7.2820 Evaluate side-chains 54 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.0870 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.061280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041333 restraints weight = 37883.251| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.92 r_work: 0.2659 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9477 Z= 0.104 Angle : 0.542 13.853 12954 Z= 0.265 Chirality : 0.041 0.167 1436 Planarity : 0.003 0.034 1533 Dihedral : 13.049 101.120 1476 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.61 % Rotamer: Outliers : 1.58 % Allowed : 14.09 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.28), residues: 1046 helix: 2.57 (0.25), residues: 466 sheet: 0.99 (0.46), residues: 137 loop : 0.47 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 682 TYR 0.007 0.001 TYR C 732 PHE 0.010 0.001 PHE C 642 TRP 0.005 0.001 TRP C 746 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 9471) covalent geometry : angle 0.50261 / 0.26 (12942) hydrogen bonds : bond 0.03197 / 2.24 ( 416) hydrogen bonds : angle 4.04938 / 2.85 ( 1198) metal coordination : bond 0.00346 / 0.17 ( 4) metal coordination : angle 6.65706 / 3.67 ( 12) Misc. bond : bond 0.00082 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.59 seconds wall clock time: 35 minutes 59.79 seconds (2159.79 seconds total)