Starting phenix.real_space_refine on Fri Feb 14 04:14:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d96_27256/02_2025/8d96_27256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d96_27256/02_2025/8d96_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_27256/02_2025/8d96_27256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d96_27256/02_2025/8d96_27256.map" model { file = "/net/cci-nas-00/data/ceres_data/8d96_27256/02_2025/8d96_27256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d96_27256/02_2025/8d96_27256.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.05, per 1000 atoms: 0.66 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 2.80 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: 3.29 Time building geometry restraints manager: 2.90 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=" 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=" C8 GTP E 1 " pdb=" N7 GTP E 1 " ideal model delta sigma weight residual 1.350 1.311 0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C4' GTP E 1 " pdb=" O4' GTP E 1 " ideal model delta sigma weight residual 1.410 1.448 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C5 GTP E 1 " pdb=" N7 GTP E 1 " ideal model delta sigma weight residual 1.350 1.387 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" O5' G E 2 " pdb=" C5' G E 2 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.26e+00 ... (remaining 9466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 12776 2.08 - 4.15: 133 4.15 - 6.23: 24 6.23 - 8.31: 6 8.31 - 10.39: 6 Bond angle restraints: 12945 Sorted by residual: angle pdb=" O1B GTP E 1 " pdb=" PB GTP E 1 " pdb=" O2B GTP E 1 " ideal model delta sigma weight residual 109.50 119.89 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C2' GTP E 1 " pdb=" C3' GTP E 1 " pdb=" C4' GTP E 1 " ideal model delta sigma weight residual 111.00 100.80 10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C1' GTP E 1 " pdb=" C2' GTP E 1 " pdb=" C3' GTP E 1 " ideal model delta sigma weight residual 111.00 100.92 10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C3' G E 2 " pdb=" O3' G E 2 " pdb=" P C E 3 " ideal model delta sigma weight residual 120.20 115.47 4.73 1.50e+00 4.44e-01 9.95e+00 angle pdb=" CA MET B 430 " pdb=" CB MET B 430 " pdb=" CG MET B 430 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.61e+00 ... (remaining 12940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 5398 31.27 - 62.53: 282 62.53 - 93.80: 39 93.80 - 125.06: 1 125.06 - 156.33: 3 Dihedral angle restraints: 5723 sinusoidal: 2626 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 5720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1318 0.072 - 0.144: 113 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: 0.860 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.920 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 : 0.002 0.051 9471 Z= 0.154 Angle : 0.583 10.386 12945 Z= 0.303 Chirality : 0.040 0.361 1436 Planarity : 0.002 0.024 1533 Dihedral : 17.809 156.329 3719 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.003 0.001 TRP C1160 HIS 0.010 0.001 HIS B 303 PHE 0.017 0.001 PHE C 642 TYR 0.014 0.001 TYR C 596 ARG 0.001 0.000 ARG B 296 *********************** 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 : 1.016 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.2899 time to fit residues: 19.7420 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 : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 322 GLN B 348 ASN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.041752 restraints weight = 37568.777| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.95 r_work: 0.2682 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9471 Z= 0.186 Angle : 0.511 6.839 12945 Z= 0.271 Chirality : 0.041 0.123 1436 Planarity : 0.003 0.025 1533 Dihedral : 15.762 175.467 1541 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 11.57 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.28), residues: 1046 helix: 2.46 (0.24), residues: 468 sheet: 1.02 (0.48), residues: 137 loop : 0.44 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 366 HIS 0.003 0.001 HIS B 300 PHE 0.012 0.001 PHE C 341 TYR 0.013 0.001 TYR B 347 ARG 0.003 0.000 ARG B 296 *********************** 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 61 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 553 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.7953 (t70) outliers start: 19 outliers final: 8 residues processed: 58 average time/residue: 0.2248 time to fit residues: 19.0111 Evaluate side-chains 49 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 1035 LEU 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 77 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3449 r_free = 0.3449 target = 0.061777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.041653 restraints weight = 37255.356| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.92 r_work: 0.2693 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9471 Z= 0.176 Angle : 0.485 6.918 12945 Z= 0.255 Chirality : 0.040 0.120 1436 Planarity : 0.003 0.027 1533 Dihedral : 15.128 144.570 1541 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 1.58 % Allowed : 12.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.28), residues: 1046 helix: 2.45 (0.24), residues: 467 sheet: 0.97 (0.47), residues: 138 loop : 0.46 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C1160 HIS 0.002 0.001 HIS C1154 PHE 0.016 0.001 PHE C 642 TYR 0.007 0.001 TYR C 732 ARG 0.002 0.000 ARG B 359 *********************** 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 57 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 553 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.7985 (t70) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.2314 time to fit residues: 17.6548 Evaluate side-chains 52 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 453 ARG 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 1035 LEU Chi-restraints excluded: chain C residue 1155 VAL 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 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.0030 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3447 r_free = 0.3447 target = 0.062073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042006 restraints weight = 37597.647| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.95 r_work: 0.2717 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9471 Z= 0.132 Angle : 0.464 6.420 12945 Z= 0.245 Chirality : 0.039 0.126 1436 Planarity : 0.003 0.028 1533 Dihedral : 14.512 107.048 1541 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.10 % Favored : 97.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.28), residues: 1046 helix: 2.50 (0.24), residues: 467 sheet: 0.99 (0.46), residues: 138 loop : 0.53 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1160 HIS 0.002 0.000 HIS B 388 PHE 0.017 0.001 PHE C 642 TYR 0.006 0.001 TYR C 732 ARG 0.002 0.000 ARG B 306 *********************** 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 56 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 553 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.7982 (t70) REVERT: C 686 CYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8541 (p) REVERT: C 990 MET cc_start: 0.8906 (tmm) cc_final: 0.8659 (tmm) outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 0.2481 time to fit residues: 18.5807 Evaluate side-chains 52 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 453 ARG 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 1248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 HIS ** 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 = 0.3396 r_free = 0.3396 target = 0.060090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039971 restraints weight = 38183.903| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.91 r_work: 0.2650 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9471 Z= 0.250 Angle : 0.518 6.805 12945 Z= 0.270 Chirality : 0.040 0.125 1436 Planarity : 0.003 0.031 1533 Dihedral : 14.433 101.241 1541 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 2.00 % Allowed : 13.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.28), residues: 1046 helix: 2.44 (0.25), residues: 473 sheet: 0.92 (0.46), residues: 137 loop : 0.42 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1160 HIS 0.004 0.001 HIS C1154 PHE 0.012 0.001 PHE B 447 TYR 0.008 0.001 TYR C 452 ARG 0.004 0.000 ARG C 688 *********************** 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 : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 GLU cc_start: 0.9386 (pm20) cc_final: 0.9168 (pm20) REVERT: C 682 ARG cc_start: 0.8519 (tpt170) cc_final: 0.8143 (mmm-85) REVERT: C 686 CYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8629 (p) REVERT: C 990 MET cc_start: 0.8871 (tmm) cc_final: 0.8619 (tmm) outliers start: 19 outliers final: 13 residues processed: 54 average time/residue: 0.2411 time to fit residues: 18.8875 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 : 1.070 ------------------------------------------------------------------------------- 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 453 ARG 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 91 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 23 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3427 r_free = 0.3427 target = 0.061028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041059 restraints weight = 37057.096| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.91 r_work: 0.2673 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9471 Z= 0.157 Angle : 0.473 6.885 12945 Z= 0.249 Chirality : 0.039 0.126 1436 Planarity : 0.003 0.032 1533 Dihedral : 14.259 100.548 1541 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.10 % Favored : 97.71 % Rotamer: Outliers : 1.89 % Allowed : 13.67 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.28), residues: 1046 helix: 2.56 (0.24), residues: 467 sheet: 0.96 (0.46), residues: 137 loop : 0.52 (0.33), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 746 HIS 0.002 0.000 HIS C1154 PHE 0.012 0.001 PHE C 642 TYR 0.007 0.001 TYR C 732 ARG 0.002 0.000 ARG C 688 *********************** 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: 18 poor density : 42 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9146 (tt) REVERT: C 686 CYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8613 (p) REVERT: C 990 MET cc_start: 0.8879 (tmm) cc_final: 0.8610 (tmm) outliers start: 18 outliers final: 13 residues processed: 56 average time/residue: 0.2276 time to fit residues: 18.7868 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 : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 432 HIS Chi-restraints excluded: chain B residue 453 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 0.0020 chunk 76 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3427 r_free = 0.3427 target = 0.061328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.041300 restraints weight = 38564.943| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.95 r_work: 0.2696 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9471 Z= 0.135 Angle : 0.474 8.036 12945 Z= 0.248 Chirality : 0.039 0.126 1436 Planarity : 0.003 0.032 1533 Dihedral : 14.144 99.992 1541 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 13.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.28), residues: 1046 helix: 2.59 (0.24), residues: 467 sheet: 1.02 (0.46), residues: 138 loop : 0.55 (0.33), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1160 HIS 0.002 0.000 HIS C1154 PHE 0.011 0.001 PHE B 447 TYR 0.006 0.001 TYR C 732 ARG 0.001 0.000 ARG C 688 *********************** 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 59 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 686 CYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8582 (p) REVERT: C 990 MET cc_start: 0.8821 (tmm) cc_final: 0.8583 (tmm) outliers start: 19 outliers final: 13 residues processed: 55 average time/residue: 0.2399 time to fit residues: 19.8578 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 : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain B residue 453 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0040 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 30.0000 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 52 optimal weight: 0.0570 chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.5110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3438 r_free = 0.3438 target = 0.061816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.041788 restraints weight = 38595.536| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 4.03 r_work: 0.2705 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9471 Z= 0.129 Angle : 0.483 9.731 12945 Z= 0.251 Chirality : 0.039 0.130 1436 Planarity : 0.003 0.030 1533 Dihedral : 14.068 99.118 1541 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.28), residues: 1046 helix: 2.62 (0.24), residues: 468 sheet: 1.05 (0.46), residues: 138 loop : 0.61 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1160 HIS 0.003 0.000 HIS B 432 PHE 0.011 0.001 PHE B 447 TYR 0.006 0.001 TYR C 732 ARG 0.001 0.000 ARG B 453 *********************** 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 61 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9134 (tt) REVERT: B 387 ARG cc_start: 0.9584 (tpt90) cc_final: 0.9284 (tpt90) REVERT: C 410 MET cc_start: 0.8460 (tpt) cc_final: 0.8152 (tpt) REVERT: C 686 CYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8567 (p) REVERT: C 990 MET cc_start: 0.8891 (tmm) cc_final: 0.8612 (tmm) outliers start: 17 outliers final: 13 residues processed: 58 average time/residue: 0.2623 time to fit residues: 21.1575 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 : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 374 ASN 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 402 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3418 r_free = 0.3418 target = 0.060580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.040686 restraints weight = 37566.594| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.87 r_work: 0.2660 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9471 Z= 0.243 Angle : 0.528 7.524 12945 Z= 0.275 Chirality : 0.041 0.186 1436 Planarity : 0.003 0.032 1533 Dihedral : 14.186 96.630 1541 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 1.79 % Allowed : 13.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.28), residues: 1046 helix: 2.53 (0.25), residues: 474 sheet: 0.63 (0.43), residues: 154 loop : 0.49 (0.34), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1160 HIS 0.004 0.001 HIS C1154 PHE 0.012 0.001 PHE B 428 TYR 0.007 0.001 TYR C 452 ARG 0.001 0.000 ARG C1167 *********************** 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 : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 MET cc_start: 0.9003 (mtp) cc_final: 0.8452 (mtp) REVERT: B 387 ARG cc_start: 0.9585 (tpt90) cc_final: 0.9274 (tpt90) REVERT: C 384 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: C 686 CYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8548 (p) REVERT: C 797 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8948 (m-80) REVERT: C 990 MET cc_start: 0.8829 (tmm) cc_final: 0.8583 (tmm) outliers start: 17 outliers final: 12 residues processed: 54 average time/residue: 0.2422 time to fit residues: 18.8236 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 : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 453 ARG 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 797 TYR 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 72 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 0.0020 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 52 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3444 r_free = 0.3444 target = 0.061696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.041932 restraints weight = 37752.291| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.91 r_work: 0.2706 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9471 Z= 0.134 Angle : 0.493 7.734 12945 Z= 0.258 Chirality : 0.040 0.150 1436 Planarity : 0.003 0.031 1533 Dihedral : 14.109 96.251 1541 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 1.68 % Allowed : 13.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.28), residues: 1046 helix: 2.65 (0.24), residues: 468 sheet: 0.93 (0.46), residues: 138 loop : 0.58 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 746 HIS 0.002 0.000 HIS B 292 PHE 0.011 0.001 PHE C 642 TYR 0.006 0.001 TYR C 732 ARG 0.002 0.000 ARG C1167 ********************** 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 56 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 MET cc_start: 0.8998 (mtp) cc_final: 0.8475 (mtp) REVERT: B 318 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9146 (tt) REVERT: B 387 ARG cc_start: 0.9579 (tpt90) cc_final: 0.9312 (tpt90) REVERT: C 410 MET cc_start: 0.8396 (tpt) cc_final: 0.8097 (tpt) REVERT: C 686 CYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8527 (p) REVERT: C 985 MET cc_start: 0.9054 (mmm) cc_final: 0.8823 (tpp) REVERT: C 990 MET cc_start: 0.8854 (tmm) cc_final: 0.8591 (tmm) outliers start: 16 outliers final: 13 residues processed: 53 average time/residue: 0.2446 time to fit residues: 18.8410 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 : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 453 ARG 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 12 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.060255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.040406 restraints weight = 37415.210| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.83 r_work: 0.2658 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9471 Z= 0.223 Angle : 0.524 7.492 12945 Z= 0.273 Chirality : 0.041 0.158 1436 Planarity : 0.003 0.032 1533 Dihedral : 14.185 94.816 1541 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.28), residues: 1046 helix: 2.56 (0.24), residues: 474 sheet: 0.69 (0.43), residues: 154 loop : 0.48 (0.34), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1160 HIS 0.003 0.001 HIS C1154 PHE 0.011 0.001 PHE B 447 TYR 0.007 0.001 TYR C 452 ARG 0.001 0.000 ARG C 650 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4122.51 seconds wall clock time: 74 minutes 5.31 seconds (4445.31 seconds total)