Starting phenix.real_space_refine on Wed Feb 14 12:01:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d96_27256/02_2024/8d96_27256_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d96_27256/02_2024/8d96_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d96_27256/02_2024/8d96_27256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d96_27256/02_2024/8d96_27256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d96_27256/02_2024/8d96_27256_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d96_27256/02_2024/8d96_27256_updated.pdb" } 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 Residue "B GLU 321": "OE1" <-> "OE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 5.77, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.5 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... running ksdssp... Secondary structure from input PDB file: 43 helices and 6 sheets defined 43.1% alpha, 14.2% beta 2 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.929A pdb=" N GLN B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 421 through 431 Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'C' and resid 410 through 419 Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 523 through 525 No H-bonds generated for 'chain 'C' and resid 523 through 525' Processing helix chain 'C' and resid 598 through 605 Processing helix chain 'C' and resid 615 through 629 Processing helix chain 'C' and resid 643 through 654 Processing helix chain 'C' and resid 659 through 662 removed outlier: 3.512A pdb=" N ILE C 662 " --> pdb=" O TRP C 659 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 659 through 662' Processing helix chain 'C' and resid 680 through 684 Processing helix chain 'C' and resid 693 through 700 Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'C' and resid 726 through 732 removed outlier: 3.691A pdb=" N GLN C 729 " --> pdb=" O GLU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 759 Processing helix chain 'C' and resid 761 through 772 Processing helix chain 'C' and resid 776 through 781 removed outlier: 4.052A pdb=" N MET C 781 " --> pdb=" O SER C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 798 Processing helix chain 'C' and resid 864 through 872 Processing helix chain 'C' and resid 910 through 930 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) Processing helix chain 'C' and resid 936 through 961 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) removed outlier: 3.992A pdb=" N GLY C 961 " --> pdb=" O TYR C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 994 removed outlier: 3.828A pdb=" N MET C 994 " --> pdb=" O MET C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1032 removed outlier: 4.188A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1080 No H-bonds generated for 'chain 'C' and resid 1078 through 1080' Processing helix chain 'C' and resid 1086 through 1100 Processing helix chain 'C' and resid 1105 through 1125 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 1130 through 1133 Processing helix chain 'C' and resid 1143 through 1145 No H-bonds generated for 'chain 'C' and resid 1143 through 1145' Processing helix chain 'C' and resid 1153 through 1164 Processing helix chain 'C' and resid 1188 through 1190 No H-bonds generated for 'chain 'C' and resid 1188 through 1190' Processing helix chain 'C' and resid 1195 through 1200 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) No H-bonds generated for 'chain 'C' and resid 1195 through 1200' Processing helix chain 'C' and resid 1208 through 1214 Processing helix chain 'C' and resid 1216 through 1223 Processing helix chain 'C' and resid 1232 through 1239 Processing sheet with id= A, first strand: chain 'C' and resid 526 through 529 removed outlier: 4.177A pdb=" N TRP C 498 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS C 497 " --> pdb=" O TRP C 345 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP C 345 " --> pdb=" O CYS C 497 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 341 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS C 342 " --> pdb=" O TRP C 366 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP C 366 " --> pdb=" O HIS C 342 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C 362 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA C 348 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE C 360 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 367 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 372 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 516 " --> pdb=" O CYS C 377 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N MET C 379 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA C 518 " --> pdb=" O MET C 379 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LYS C 381 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA C 520 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing sheet with id= B, 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= C, first strand: chain 'C' and resid 689 through 692 removed outlier: 3.502A pdb=" N PHE C 542 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 559 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET C 547 " --> pdb=" O ILE C 557 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE C 557 " --> pdb=" O MET C 547 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN C 549 " --> pdb=" O ASN C 555 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASN C 555 " --> pdb=" O ASN C 549 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE C 558 " --> pdb=" O SER C 587 " (cutoff:3.500A) Processing sheet with id= D, 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: 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= E, first strand: chain 'C' and resid 1038 through 1044 removed outlier: 7.250A pdb=" N LEU C 858 " --> pdb=" O ASP C1041 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL C1043 " --> pdb=" O ILE C 856 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 856 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C1008 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR C1000 " --> pdb=" O MET C1007 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN C1009 " --> pdb=" O VAL C 998 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 998 " --> pdb=" O ASN C1009 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 1135 through 1138 354 hydrogen bonds defined for protein. 1035 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: 3.20 Time building geometry restraints manager: 4.39 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: 73.69 - 86.90: 12 86.90 - 100.12: 2 100.12 - 113.33: 5601 113.33 - 126.55: 7104 126.55 - 139.76: 226 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: 5684 3.06 - 3.67: 13595 3.67 - 4.29: 18996 4.29 - 4.90: 32010 Nonbonded interactions: 70309 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 2.440 nonbonded pdb=" OD1 ASN B 348 " pdb=" N4 DC F 17 " model vdw 1.845 2.520 nonbonded pdb=" NE2 HIS B 300 " pdb=" O2G GTP E 1 " model vdw 2.005 2.520 nonbonded pdb=" CE1 HIS B 300 " pdb=" O2G GTP E 1 " model vdw 2.009 2.608 ... (remaining 70304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.630 Find NCS groups from input model: 0.250 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- 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= 0.147 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 fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.073 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.2814 time to fit residues: 19.0942 Evaluate side-chains 39 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9471 Z= 0.157 Angle : 0.490 7.312 12945 Z= 0.254 Chirality : 0.040 0.140 1436 Planarity : 0.003 0.062 1533 Dihedral : 15.618 177.452 1541 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.77 % Favored : 97.04 % Rotamer: Outliers : 1.58 % Allowed : 12.20 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.28), residues: 1046 helix: 2.26 (0.24), residues: 476 sheet: 0.70 (0.44), residues: 147 loop : 0.45 (0.34), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 366 HIS 0.013 0.001 HIS C1250 PHE 0.019 0.001 PHE C 642 TYR 0.016 0.001 TYR B 347 ARG 0.005 0.000 ARG B 387 *********************** 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 fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 1.065 Fit side-chains REVERT: B 307 MET cc_start: 0.8237 (mtp) cc_final: 0.8010 (mtp) REVERT: B 321 GLU cc_start: 0.9257 (pm20) cc_final: 0.8965 (pm20) REVERT: B 322 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: C 544 MET cc_start: 0.9381 (ptp) cc_final: 0.8990 (ptt) outliers start: 15 outliers final: 6 residues processed: 53 average time/residue: 0.2319 time to fit residues: 17.8799 Evaluate side-chains 47 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 374 ASN 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 1248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9471 Z= 0.331 Angle : 0.546 7.046 12945 Z= 0.284 Chirality : 0.042 0.127 1436 Planarity : 0.003 0.027 1533 Dihedral : 15.465 145.864 1541 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.46 % Rotamer: Outliers : 1.79 % Allowed : 13.99 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.28), residues: 1046 helix: 2.24 (0.25), residues: 474 sheet: 0.49 (0.44), residues: 149 loop : 0.18 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 746 HIS 0.004 0.001 HIS C1154 PHE 0.015 0.001 PHE C 341 TYR 0.012 0.001 TYR C 452 ARG 0.007 0.001 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8112 (mtp) cc_final: 0.7820 (mtp) REVERT: C 544 MET cc_start: 0.9371 (ptp) cc_final: 0.9019 (ptt) REVERT: C 990 MET cc_start: 0.8769 (tmm) cc_final: 0.8471 (tmm) outliers start: 17 outliers final: 8 residues processed: 53 average time/residue: 0.2294 time to fit residues: 17.8787 Evaluate side-chains 49 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN 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 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 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1489 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= 0.150 Angle : 0.459 6.522 12945 Z= 0.241 Chirality : 0.039 0.126 1436 Planarity : 0.003 0.026 1533 Dihedral : 14.532 106.413 1541 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 1.58 % Allowed : 14.41 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.28), residues: 1046 helix: 2.32 (0.25), residues: 472 sheet: 0.79 (0.47), residues: 132 loop : 0.29 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1160 HIS 0.002 0.000 HIS B 432 PHE 0.011 0.001 PHE B 447 TYR 0.007 0.001 TYR B 427 ARG 0.002 0.000 ARG C1167 *********************** 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 fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 553 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7817 (t70) REVERT: C 686 CYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8324 (p) REVERT: C 990 MET cc_start: 0.8726 (tmm) cc_final: 0.8444 (tmm) outliers start: 15 outliers final: 9 residues processed: 52 average time/residue: 0.2346 time to fit residues: 17.7147 Evaluate side-chains 51 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain B residue 433 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9471 Z= 0.224 Angle : 0.486 6.603 12945 Z= 0.253 Chirality : 0.040 0.128 1436 Planarity : 0.003 0.026 1533 Dihedral : 14.409 101.850 1541 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.87 % Favored : 96.94 % Rotamer: Outliers : 1.79 % Allowed : 14.30 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.28), residues: 1046 helix: 2.39 (0.25), residues: 468 sheet: 0.65 (0.44), residues: 149 loop : 0.34 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1160 HIS 0.003 0.000 HIS C1154 PHE 0.011 0.001 PHE B 447 TYR 0.007 0.001 TYR C 452 ARG 0.003 0.000 ARG C 682 *********************** 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 57 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 40 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8111 (mtp) cc_final: 0.7758 (mtp) REVERT: B 321 GLU cc_start: 0.9261 (pm20) cc_final: 0.9018 (pm20) REVERT: C 686 CYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8534 (p) REVERT: C 990 MET cc_start: 0.8719 (tmm) cc_final: 0.8402 (tmm) outliers start: 17 outliers final: 11 residues processed: 52 average time/residue: 0.2171 time to fit residues: 16.9283 Evaluate side-chains 50 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 1119 ILE 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 92 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1735 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= 0.160 Angle : 0.458 6.840 12945 Z= 0.240 Chirality : 0.039 0.123 1436 Planarity : 0.003 0.026 1533 Dihedral : 14.347 100.616 1541 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 2.10 % Allowed : 13.88 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.28), residues: 1046 helix: 2.41 (0.25), residues: 467 sheet: 0.59 (0.44), residues: 149 loop : 0.31 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C1160 HIS 0.002 0.000 HIS C1217 PHE 0.011 0.001 PHE B 447 TYR 0.006 0.001 TYR C 968 ARG 0.001 0.000 ARG C 682 *********************** 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 61 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 41 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8113 (mtp) cc_final: 0.7782 (mtp) REVERT: C 553 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.7838 (t70) REVERT: C 682 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8188 (tpt90) REVERT: C 686 CYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8542 (p) REVERT: C 990 MET cc_start: 0.8703 (tmm) cc_final: 0.8420 (tmm) outliers start: 20 outliers final: 12 residues processed: 56 average time/residue: 0.2276 time to fit residues: 18.5412 Evaluate side-chains 56 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 553 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 686 CYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 0.0370 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1771 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= 0.140 Angle : 0.451 6.776 12945 Z= 0.236 Chirality : 0.039 0.124 1436 Planarity : 0.003 0.026 1533 Dihedral : 14.296 99.712 1541 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.87 % Favored : 96.94 % Rotamer: Outliers : 1.89 % Allowed : 13.88 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.28), residues: 1046 helix: 2.44 (0.25), residues: 467 sheet: 0.69 (0.45), residues: 148 loop : 0.31 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 746 HIS 0.002 0.000 HIS C1154 PHE 0.011 0.001 PHE B 447 TYR 0.005 0.001 TYR C 968 ARG 0.001 0.000 ARG C 682 *********************** 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 fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8104 (mtp) cc_final: 0.7756 (mtp) REVERT: B 321 GLU cc_start: 0.9217 (pm20) cc_final: 0.8917 (pm20) REVERT: C 384 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: C 553 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.7836 (t70) REVERT: C 682 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8186 (tpt90) REVERT: C 686 CYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8435 (p) REVERT: C 990 MET cc_start: 0.8690 (tmm) cc_final: 0.8390 (tmm) outliers start: 18 outliers final: 12 residues processed: 55 average time/residue: 0.2241 time to fit residues: 17.9578 Evaluate side-chains 55 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 384 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 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 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.0040 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1797 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= 0.138 Angle : 0.450 6.690 12945 Z= 0.234 Chirality : 0.039 0.133 1436 Planarity : 0.003 0.026 1533 Dihedral : 14.235 98.702 1541 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.58 % Favored : 97.23 % Rotamer: Outliers : 2.00 % Allowed : 13.99 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.28), residues: 1046 helix: 2.46 (0.25), residues: 467 sheet: 0.62 (0.44), residues: 149 loop : 0.37 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 746 HIS 0.002 0.000 HIS C 565 PHE 0.011 0.001 PHE B 447 TYR 0.005 0.001 TYR B 427 ARG 0.001 0.000 ARG C 688 *********************** 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 fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8103 (mtp) cc_final: 0.7720 (mtp) REVERT: B 321 GLU cc_start: 0.9264 (pm20) cc_final: 0.8949 (pm20) REVERT: C 553 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.7861 (t70) REVERT: C 682 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8312 (mmm-85) REVERT: C 686 CYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8318 (p) REVERT: C 990 MET cc_start: 0.8690 (tmm) cc_final: 0.8384 (tmm) outliers start: 19 outliers final: 12 residues processed: 57 average time/residue: 0.2308 time to fit residues: 19.1967 Evaluate side-chains 55 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1858 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= 0.133 Angle : 0.452 6.654 12945 Z= 0.236 Chirality : 0.039 0.145 1436 Planarity : 0.003 0.026 1533 Dihedral : 14.167 98.017 1541 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.87 % Favored : 96.94 % Rotamer: Outliers : 2.00 % Allowed : 14.09 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.48 (0.25), residues: 468 sheet: 0.63 (0.44), residues: 148 loop : 0.36 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 746 HIS 0.002 0.000 HIS C 565 PHE 0.009 0.001 PHE B 447 TYR 0.006 0.001 TYR B 427 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 60 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8097 (mtp) cc_final: 0.7700 (mtp) REVERT: B 321 GLU cc_start: 0.9246 (pm20) cc_final: 0.8922 (pm20) REVERT: C 553 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.7847 (t70) REVERT: C 682 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8324 (mmm-85) REVERT: C 686 CYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8316 (p) REVERT: C 990 MET cc_start: 0.8683 (tmm) cc_final: 0.8378 (tmm) outliers start: 19 outliers final: 12 residues processed: 56 average time/residue: 0.2402 time to fit residues: 19.6438 Evaluate side-chains 54 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 61 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9471 Z= 0.276 Angle : 0.521 6.512 12945 Z= 0.270 Chirality : 0.041 0.160 1436 Planarity : 0.003 0.026 1533 Dihedral : 14.380 94.863 1541 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.46 % Rotamer: Outliers : 1.68 % Allowed : 14.51 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.28), residues: 1046 helix: 2.39 (0.25), residues: 468 sheet: 0.59 (0.44), residues: 147 loop : 0.24 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 746 HIS 0.003 0.001 HIS C1217 PHE 0.011 0.001 PHE C 341 TYR 0.009 0.001 TYR C 452 ARG 0.004 0.000 ARG C 945 ********************** 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 58 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: B 288 MET cc_start: 0.8641 (mtp) cc_final: 0.8388 (mtp) REVERT: B 307 MET cc_start: 0.8179 (mtp) cc_final: 0.7770 (mtp) REVERT: B 321 GLU cc_start: 0.9266 (pm20) cc_final: 0.8945 (pm20) REVERT: C 384 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: C 544 MET cc_start: 0.9211 (ptt) cc_final: 0.8895 (ptt) REVERT: C 990 MET cc_start: 0.8709 (tmm) cc_final: 0.8370 (tmm) outliers start: 16 outliers final: 12 residues processed: 55 average time/residue: 0.2291 time to fit residues: 18.4993 Evaluate side-chains 54 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 844 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 442 ASN 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 = 0.060703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.040787 restraints weight = 37423.803| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.82 r_work: 0.2684 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2032 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= 0.147 Angle : 0.461 6.724 12945 Z= 0.240 Chirality : 0.040 0.161 1436 Planarity : 0.003 0.025 1533 Dihedral : 14.212 94.509 1541 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.06 % Favored : 96.75 % Rotamer: Outliers : 1.47 % Allowed : 14.62 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.28), residues: 1046 helix: 2.47 (0.25), residues: 468 sheet: 0.83 (0.46), residues: 132 loop : 0.34 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 746 HIS 0.002 0.000 HIS C 565 PHE 0.010 0.001 PHE B 447 TYR 0.006 0.001 TYR B 427 ARG 0.001 0.000 ARG C 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.83 seconds wall clock time: 33 minutes 7.84 seconds (1987.84 seconds total)