Starting phenix.real_space_refine on Thu Jul 2 18:46:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d96_27256/07_2026/8d96_27256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d96_27256/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2026/8d96_27256.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2026/8d96_27256.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2026/8d96_27256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2026/8d96_27256.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2026/8d96_27256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2026/8d96_27256.map" } 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-dev-6108/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, 'RNA': 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: 1.58, per 1000 atoms: 0.17 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: 0.69 Conformation dependent library (CDL) restraints added in 195.9 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: 0.73 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: 1.24 Time building geometry restraints manager: 0.87 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: 12763 2.08 - 4.15: 146 4.15 - 6.23: 24 6.23 - 8.31: 6 8.31 - 10.39: 6 Bond angle restraints: 12945 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 12940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 5362 31.27 - 62.53: 268 62.53 - 93.80: 26 93.80 - 125.06: 1 125.06 - 156.33: 3 Dihedral angle restraints: 5660 sinusoidal: 2563 harmonic: 3097 Sorted by residual: dihedral pdb=" C5' GTP E 1 " pdb=" O5' GTP E 1 " pdb=" PA GTP E 1 " pdb=" O3A GTP E 1 " ideal model delta sinusoidal sigma weight residual 69.27 -87.06 156.33 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O3B GTP E 1 " pdb=" O3A GTP E 1 " pdb=" PB GTP E 1 " pdb=" PA GTP E 1 " ideal model delta sinusoidal sigma weight residual 291.08 154.30 136.78 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" O5' GTP E 1 " pdb=" O3A GTP E 1 " pdb=" PA GTP E 1 " pdb=" PB GTP E 1 " ideal model delta sinusoidal sigma weight residual -85.88 41.35 -127.22 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 5657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1302 0.072 - 0.144: 129 0.144 - 0.217: 4 0.217 - 0.289: 0 0.289 - 0.361: 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 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C3' GTP E 1 " pdb=" C2' GTP E 1 " pdb=" C4' GTP E 1 " pdb=" O3' GTP E 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" C3' G E 2 " pdb=" C4' G E 2 " pdb=" O3' G E 2 " pdb=" C2' G E 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.47e-01 ... (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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.800 ------------------------------------------------------------------------------- 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= 0.421 Angle : 0.617 10.386 12957 Z= 0.353 Chirality : 0.041 0.361 1436 Planarity : 0.002 0.024 1533 Dihedral : 17.218 156.329 3656 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 0.00274 / 0.20 ( 9471) covalent geometry : angle 0.60195 / 0.35 (12945) 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 : 0.236 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.1087 time to fit residues: 7.3260 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 : 0.242 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.061250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.040894 restraints weight = 37820.620| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.97 r_work: 0.2649 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9477 Z= 0.182 Angle : 0.586 9.451 12957 Z= 0.302 Chirality : 0.042 0.219 1436 Planarity : 0.004 0.082 1533 Dihedral : 14.111 171.115 1478 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.96 % Favored : 96.85 % Rotamer: Outliers : 1.58 % Allowed : 12.72 % Favored : 85.70 % 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: 1.82 (0.28), residues: 1046 helix: 2.20 (0.24), residues: 480 sheet: 0.66 (0.44), residues: 152 loop : 0.33 (0.34), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 387 TYR 0.016 0.001 TYR B 362 PHE 0.017 0.001 PHE C 642 TRP 0.007 0.001 TRP C 659 HIS 0.011 0.001 HIS C1250 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 9471) covalent geometry : angle 0.57020 / 0.30 (12945) hydrogen bonds : bond 0.04641 / 3.27 ( 416) hydrogen bonds : angle 4.72592 / 3.33 ( 1198) metal coordination : bond 0.00766 / 0.38 ( 4) metal coordination : angle 4.49263 / 2.08 ( 12) Misc. bond : bond 0.00747 / 0.36 ( 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 57 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 54 average time/residue: 0.0816 time to fit residues: 6.3805 Evaluate side-chains 46 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 MET 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: 0.7980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 0.0570 chunk 105 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.061850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.041696 restraints weight = 37756.583| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.87 r_work: 0.2707 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9477 Z= 0.107 Angle : 0.501 9.036 12957 Z= 0.260 Chirality : 0.040 0.145 1436 Planarity : 0.003 0.027 1533 Dihedral : 13.924 169.364 1478 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 1.79 % Allowed : 12.93 % Favored : 85.28 % 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: 2.04 (0.28), residues: 1046 helix: 2.36 (0.24), residues: 466 sheet: 1.06 (0.47), residues: 137 loop : 0.44 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 682 TYR 0.008 0.001 TYR B 347 PHE 0.019 0.001 PHE C 642 TRP 0.005 0.001 TRP C1160 HIS 0.004 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 9471) covalent geometry : angle 0.48195 / 0.26 (12945) hydrogen bonds : bond 0.03734 / 2.68 ( 416) hydrogen bonds : angle 4.40915 / 3.11 ( 1198) metal coordination : bond 0.00383 / 0.19 ( 4) metal coordination : angle 4.49358 / 2.19 ( 12) Misc. bond : bond 0.00169 / 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 59 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.283 Fit side-chains REVERT: B 307 MET cc_start: 0.9340 (mtp) cc_final: 0.9032 (mtp) REVERT: B 450 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.7835 (tp30) REVERT: C 553 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.7973 (t70) REVERT: C 686 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8640 (p) outliers start: 17 outliers final: 7 residues processed: 55 average time/residue: 0.0940 time to fit residues: 7.5296 Evaluate side-chains 49 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 450 GLU 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 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: 0.9980 chunk 15 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 396 GLN ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.060182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.040262 restraints weight = 38417.458| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.81 r_work: 0.2665 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9477 Z= 0.202 Angle : 0.564 9.452 12957 Z= 0.289 Chirality : 0.042 0.147 1436 Planarity : 0.003 0.033 1533 Dihedral : 13.598 153.951 1478 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.96 % Favored : 96.85 % Rotamer: Outliers : 2.21 % Allowed : 12.93 % 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: 1.85 (0.28), residues: 1046 helix: 2.33 (0.25), residues: 467 sheet: 0.60 (0.44), residues: 153 loop : 0.32 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 453 TYR 0.011 0.001 TYR C 452 PHE 0.016 0.001 PHE C 642 TRP 0.006 0.001 TRP C1160 HIS 0.004 0.001 HIS C1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 9471) covalent geometry : angle 0.54506 / 0.29 (12945) hydrogen bonds : bond 0.04139 / 2.90 ( 416) hydrogen bonds : angle 4.39790 / 3.11 ( 1198) metal coordination : bond 0.00661 / 0.33 ( 4) metal coordination : angle 4.83775 / 2.34 ( 12) Misc. bond : bond 0.00100 / 0.05 ( 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 61 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.9306 (mtp) cc_final: 0.8924 (mtp) REVERT: C 553 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.7899 (t70) REVERT: C 686 CYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8700 (p) REVERT: C 990 MET cc_start: 0.8883 (tmm) cc_final: 0.8659 (tmm) outliers start: 21 outliers final: 12 residues processed: 58 average time/residue: 0.0825 time to fit residues: 6.7889 Evaluate side-chains 53 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 519 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 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: 4.9990 chunk 104 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 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 = 0.3408 r_free = 0.3408 target = 0.060529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.040256 restraints weight = 38369.774| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.00 r_work: 0.2659 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9477 Z= 0.140 Angle : 0.530 9.319 12957 Z= 0.273 Chirality : 0.041 0.138 1436 Planarity : 0.003 0.030 1533 Dihedral : 13.327 137.058 1478 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 2.21 % Allowed : 13.04 % 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: 1.95 (0.28), residues: 1046 helix: 2.38 (0.24), residues: 466 sheet: 0.82 (0.47), residues: 137 loop : 0.34 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.007 0.001 TYR C 732 PHE 0.014 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 0.00313 / 0.14 ( 9471) covalent geometry : angle 0.50676 / 0.27 (12945) hydrogen bonds : bond 0.03765 / 2.65 ( 416) hydrogen bonds : angle 4.31470 / 3.06 ( 1198) metal coordination : bond 0.00461 / 0.23 ( 4) metal coordination : angle 5.12088 / 2.59 ( 12) Misc. bond : bond 0.00126 / 0.06 ( 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 62 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.9299 (mtp) cc_final: 0.8895 (mtp) REVERT: C 553 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.7992 (t70) REVERT: C 686 CYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 990 MET cc_start: 0.8946 (tmm) cc_final: 0.8675 (tmm) outliers start: 21 outliers final: 12 residues processed: 56 average time/residue: 0.0865 time to fit residues: 6.9477 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 : 0.366 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 39 optimal weight: 6.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 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 = 0.3425 r_free = 0.3425 target = 0.061285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.041155 restraints weight = 38099.231| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.96 r_work: 0.2657 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9477 Z= 0.102 Angle : 0.505 9.635 12957 Z= 0.260 Chirality : 0.040 0.131 1436 Planarity : 0.003 0.031 1533 Dihedral : 12.892 106.658 1478 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 13.14 % 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: 2.06 (0.28), residues: 1046 helix: 2.45 (0.24), residues: 466 sheet: 0.90 (0.47), residues: 138 loop : 0.41 (0.33), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 682 TYR 0.008 0.001 TYR C 732 PHE 0.015 0.001 PHE C 642 TRP 0.004 0.001 TRP C1160 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 ( 9471) covalent geometry : angle 0.47946 / 0.26 (12945) hydrogen bonds : bond 0.03228 / 2.28 ( 416) hydrogen bonds : angle 4.19026 / 2.96 ( 1198) metal coordination : bond 0.00340 / 0.17 ( 4) metal coordination : angle 5.18060 / 2.69 ( 12) Misc. bond : bond 0.00162 / 0.08 ( 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 60 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.9275 (mtp) cc_final: 0.8898 (mtp) REVERT: C 553 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.7977 (t70) REVERT: C 682 ARG cc_start: 0.8519 (tpt170) cc_final: 0.8162 (mmm-85) REVERT: C 686 CYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8593 (p) REVERT: C 990 MET cc_start: 0.8898 (tmm) cc_final: 0.8658 (tmm) outliers start: 19 outliers final: 13 residues processed: 55 average time/residue: 0.0887 time to fit residues: 7.0370 Evaluate side-chains 56 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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: 30.0000 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 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: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 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 = 0.3394 r_free = 0.3394 target = 0.059995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.039783 restraints weight = 38564.328| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.94 r_work: 0.2613 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9477 Z= 0.184 Angle : 0.560 10.946 12957 Z= 0.284 Chirality : 0.041 0.144 1436 Planarity : 0.003 0.034 1533 Dihedral : 12.699 103.411 1478 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 2.10 % Allowed : 13.35 % 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: 1.88 (0.28), residues: 1046 helix: 2.37 (0.25), residues: 473 sheet: 0.58 (0.44), residues: 154 loop : 0.28 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 688 TYR 0.009 0.001 TYR C 452 PHE 0.013 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 0.00424 / 0.18 ( 9471) covalent geometry : angle 0.53391 / 0.28 (12945) hydrogen bonds : bond 0.03927 / 2.75 ( 416) hydrogen bonds : angle 4.24506 / 3.01 ( 1198) metal coordination : bond 0.00526 / 0.26 ( 4) metal coordination : angle 5.54435 / 2.83 ( 12) Misc. bond : bond 0.00068 / 0.04 ( 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 61 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: C 384 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8644 (mt-10) REVERT: C 553 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8004 (t70) REVERT: C 686 CYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8657 (p) REVERT: C 781 MET cc_start: 0.9373 (ttm) cc_final: 0.9166 (tpp) REVERT: C 990 MET cc_start: 0.8938 (tmm) cc_final: 0.8663 (tmm) outliers start: 20 outliers final: 15 residues processed: 57 average time/residue: 0.0901 time to fit residues: 7.4202 Evaluate side-chains 57 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 689 MET Chi-restraints excluded: chain C residue 776 MET 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: 3.9990 chunk 90 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 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 = 0.3411 r_free = 0.3411 target = 0.060624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.040401 restraints weight = 38008.965| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.97 r_work: 0.2660 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9477 Z= 0.118 Angle : 0.528 11.101 12957 Z= 0.269 Chirality : 0.040 0.131 1436 Planarity : 0.003 0.033 1533 Dihedral : 12.685 102.391 1478 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 13.25 % 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: 2.06 (0.28), residues: 1046 helix: 2.47 (0.24), residues: 466 sheet: 0.88 (0.46), residues: 137 loop : 0.41 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 453 TYR 0.007 0.001 TYR C 732 PHE 0.012 0.001 PHE B 447 TRP 0.005 0.001 TRP C1160 HIS 0.002 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9471) covalent geometry : angle 0.49912 / 0.27 (12945) hydrogen bonds : bond 0.03539 / 2.49 ( 416) hydrogen bonds : angle 4.17457 / 2.96 ( 1198) metal coordination : bond 0.00312 / 0.15 ( 4) metal coordination : angle 5.69325 / 2.99 ( 12) Misc. bond : bond 0.00062 / 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 57 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: C 384 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8611 (mt-10) REVERT: C 686 CYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 781 MET cc_start: 0.9364 (ttm) cc_final: 0.9157 (tpp) REVERT: C 990 MET cc_start: 0.8909 (tmm) cc_final: 0.8635 (tmm) outliers start: 18 outliers final: 14 residues processed: 53 average time/residue: 0.0731 time to fit residues: 5.8034 Evaluate side-chains 55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 384 GLU 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 776 MET 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: 0.7980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** 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 = 0.3419 r_free = 0.3419 target = 0.060979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040862 restraints weight = 38012.517| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.97 r_work: 0.2674 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9477 Z= 0.109 Angle : 0.522 11.645 12957 Z= 0.264 Chirality : 0.040 0.126 1436 Planarity : 0.003 0.032 1533 Dihedral : 12.633 101.165 1478 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 1.79 % Allowed : 13.56 % 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: 2.10 (0.28), residues: 1046 helix: 2.50 (0.24), residues: 466 sheet: 0.93 (0.46), residues: 137 loop : 0.42 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.007 0.001 TYR C 732 PHE 0.011 0.001 PHE B 447 TRP 0.004 0.001 TRP C1160 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9471) covalent geometry : angle 0.49165 / 0.26 (12945) hydrogen bonds : bond 0.03242 / 2.28 ( 416) hydrogen bonds : angle 4.10877 / 2.90 ( 1198) metal coordination : bond 0.00292 / 0.14 ( 4) metal coordination : angle 5.75009 / 3.04 ( 12) Misc. bond : bond 0.00062 / 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 57 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.207 Fit side-chains REVERT: B 307 MET cc_start: 0.9273 (mtp) cc_final: 0.8833 (mtp) REVERT: C 384 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8576 (mt-10) REVERT: C 553 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.8040 (t70) REVERT: C 686 CYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 990 MET cc_start: 0.8892 (tmm) cc_final: 0.8619 (tmm) outliers start: 17 outliers final: 11 residues processed: 54 average time/residue: 0.0680 time to fit residues: 5.4940 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 : 0.222 ------------------------------------------------------------------------------- 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 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: 0.0010 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN B 432 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.040826 restraints weight = 38264.238| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.82 r_work: 0.2679 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9477 Z= 0.134 Angle : 0.545 13.799 12957 Z= 0.272 Chirality : 0.040 0.130 1436 Planarity : 0.003 0.032 1533 Dihedral : 12.637 100.455 1478 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 1.47 % Allowed : 13.77 % 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: 2.02 (0.28), residues: 1046 helix: 2.43 (0.25), residues: 473 sheet: 0.93 (0.46), residues: 138 loop : 0.32 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 682 TYR 0.007 0.001 TYR C 452 PHE 0.012 0.001 PHE B 447 TRP 0.005 0.001 TRP C1160 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9471) covalent geometry : angle 0.50974 / 0.27 (12945) hydrogen bonds : bond 0.03449 / 2.42 ( 416) hydrogen bonds : angle 4.13266 / 2.93 ( 1198) metal coordination : bond 0.00526 / 0.27 ( 4) metal coordination : angle 6.37204 / 3.46 ( 12) Misc. bond : bond 0.00072 / 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 55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.9242 (mtp) cc_final: 0.8769 (mtp) REVERT: B 321 GLU cc_start: 0.9372 (pm20) cc_final: 0.9145 (pm20) REVERT: C 384 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8589 (mt-10) REVERT: C 686 CYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8638 (p) REVERT: C 990 MET cc_start: 0.8826 (tmm) cc_final: 0.8586 (tmm) outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.0839 time to fit residues: 6.6092 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 : 0.312 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 300 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 = 0.3426 r_free = 0.3426 target = 0.060932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.041162 restraints weight = 37755.995| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.80 r_work: 0.2657 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9477 Z= 0.110 Angle : 0.535 13.526 12957 Z= 0.268 Chirality : 0.040 0.153 1436 Planarity : 0.003 0.031 1533 Dihedral : 12.630 100.153 1478 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.20 % Favored : 97.61 % Rotamer: Outliers : 1.37 % Allowed : 13.67 % Favored : 84.96 % 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: 2.16 (0.28), residues: 1046 helix: 2.56 (0.24), residues: 466 sheet: 0.94 (0.46), residues: 137 loop : 0.46 (0.33), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1167 TYR 0.007 0.001 TYR C 732 PHE 0.034 0.001 PHE B 428 TRP 0.005 0.001 TRP C1160 HIS 0.009 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9471) covalent geometry : angle 0.49903 / 0.27 (12945) hydrogen bonds : bond 0.03357 / 2.33 ( 416) hydrogen bonds : angle 4.08756 / 2.89 ( 1198) metal coordination : bond 0.00406 / 0.20 ( 4) metal coordination : angle 6.32161 / 3.42 ( 12) Misc. bond : bond 0.00070 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1740.44 seconds wall clock time: 30 minutes 34.88 seconds (1834.88 seconds total)