Starting phenix.real_space_refine on Tue Sep 24 22:11:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/09_2024/7bv2_30210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/09_2024/7bv2_30210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/09_2024/7bv2_30210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/09_2024/7bv2_30210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/09_2024/7bv2_30210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv2_30210/09_2024/7bv2_30210.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 Zn 2 6.06 5 P 28 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5407 2.51 5 N 1437 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8630 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6712 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 805} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "T" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' MG': 2, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'F86': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1816 SG CYS A 301 49.560 64.092 38.924 1.00 12.33 S ATOM 1857 SG CYS A 306 49.369 63.471 35.242 1.00 10.05 S ATOM 1889 SG CYS A 310 52.744 63.249 37.074 1.00 9.56 S ATOM 3297 SG CYS A 487 31.730 59.229 47.521 1.00 11.38 S ATOM 4550 SG CYS A 645 30.654 59.341 44.075 1.00 12.29 S ATOM 4556 SG CYS A 646 33.652 60.861 45.159 1.00 10.15 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" O POP A1003 " occ=0.50 ... (7 atoms not shown) pdb=" P2 POP A1003 " occ=0.50 residue: pdb="MG MG A1004 " occ=0.50 residue: pdb="MG MG A1005 " occ=0.50 residue: pdb=" C1 F86 P 101 " occ=0.50 ... (22 atoms not shown) pdb=" P1 F86 P 101 " occ=0.50 Time building chain proxies: 5.54, per 1000 atoms: 0.64 Number of scatterers: 8630 At special positions: 0 Unit cell: (95.316, 93.288, 106.47, 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) Zn 2 29.99 S 58 16.00 P 28 15.00 Mg 2 11.99 O 1696 8.00 N 1437 7.00 C 5407 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 973.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 8 sheets defined 56.4% alpha, 13.4% beta 9 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.534A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.682A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.045A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.327A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.522A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.541A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.853A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.519A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.726A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.710A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.656A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 851 through 867 removed outlier: 3.958A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.207A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.306A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 100 through 109 removed outlier: 4.036A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.168A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 removed outlier: 4.043A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.827A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.094A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.653A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.653A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.653A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.688A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1344 1.29 - 1.43: 2552 1.43 - 1.56: 4834 1.56 - 1.70: 49 1.70 - 1.83: 88 Bond restraints: 8867 Sorted by residual: bond pdb=" O4 F86 P 101 " pdb=" P1 F86 P 101 " ideal model delta sigma weight residual 1.601 1.704 -0.103 1.00e-02 1.00e+04 1.06e+02 bond pdb=" C12 F86 P 101 " pdb=" N2 F86 P 101 " ideal model delta sigma weight residual 1.293 1.359 -0.066 1.00e-02 1.00e+04 4.38e+01 bond pdb=" P U P 20 " pdb=" O5' U P 20 " ideal model delta sigma weight residual 1.593 1.676 -0.083 1.50e-02 4.44e+03 3.08e+01 bond pdb=" C11 F86 P 101 " pdb=" N5 F86 P 101 " ideal model delta sigma weight residual 1.337 1.392 -0.055 1.00e-02 1.00e+04 3.07e+01 bond pdb=" O5 F86 P 101 " pdb=" P1 F86 P 101 " ideal model delta sigma weight residual 1.533 1.483 0.050 1.50e-02 4.44e+03 1.11e+01 ... (remaining 8862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 12102 3.75 - 7.50: 47 7.50 - 11.25: 5 11.25 - 15.00: 0 15.00 - 18.75: 1 Bond angle restraints: 12155 Sorted by residual: angle pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " pdb=" C11 F86 P 101 " ideal model delta sigma weight residual 136.68 128.29 8.39 1.00e+00 1.00e+00 7.04e+01 angle pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " pdb=" N1 F86 P 101 " ideal model delta sigma weight residual 107.41 115.10 -7.69 1.00e+00 1.00e+00 5.91e+01 angle pdb=" C7 F86 P 101 " pdb=" C10 F86 P 101 " pdb=" C9 F86 P 101 " ideal model delta sigma weight residual 107.84 100.22 7.62 1.00e+00 1.00e+00 5.81e+01 angle pdb=" P1 POP A1003 " pdb=" O POP A1003 " pdb=" P2 POP A1003 " ideal model delta sigma weight residual 139.66 120.91 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C5 F86 P 101 " pdb=" N1 F86 P 101 " pdb=" C9 F86 P 101 " ideal model delta sigma weight residual 109.66 105.27 4.39 1.00e+00 1.00e+00 1.93e+01 ... (remaining 12150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4697 17.97 - 35.93: 426 35.93 - 53.90: 99 53.90 - 71.87: 33 71.87 - 89.84: 9 Dihedral angle restraints: 5264 sinusoidal: 2265 harmonic: 2999 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -148.17 -31.83 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN A 611 " pdb=" C ASN A 611 " pdb=" N PRO A 612 " pdb=" CA PRO A 612 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1063 0.052 - 0.103: 258 0.103 - 0.155: 52 0.155 - 0.207: 8 0.207 - 0.258: 6 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA ARG B 111 " pdb=" N ARG B 111 " pdb=" C ARG B 111 " pdb=" CB ARG B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LYS A 676 " pdb=" N LYS A 676 " pdb=" C LYS A 676 " pdb=" CB LYS A 676 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1384 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U P 20 " 0.066 2.00e-02 2.50e+03 3.19e-02 2.29e+01 pdb=" N1 U P 20 " -0.052 2.00e-02 2.50e+03 pdb=" C2 U P 20 " -0.025 2.00e-02 2.50e+03 pdb=" O2 U P 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U P 20 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U P 20 " 0.009 2.00e-02 2.50e+03 pdb=" O4 U P 20 " 0.030 2.00e-02 2.50e+03 pdb=" C5 U P 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U P 20 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 36 " 0.017 2.00e-02 2.50e+03 1.80e-02 4.84e+00 pdb=" CG HIS C 36 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS C 36 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS C 36 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 36 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 36 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 532 " 0.011 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C LYS A 532 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 532 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 533 " 0.012 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 31 2.53 - 3.12: 6388 3.12 - 3.72: 13413 3.72 - 4.31: 20117 4.31 - 4.90: 32232 Nonbonded interactions: 72181 Sorted by model distance: nonbonded pdb=" O4 U P 12 " pdb=" N1 A T 19 " model vdw 1.942 2.496 nonbonded pdb=" O ASN A 790 " pdb=" OD1 ASN A 790 " model vdw 2.135 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.248 3.040 nonbonded pdb=" O ILE A 494 " pdb=" NE2 GLN A 573 " model vdw 2.281 3.120 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.284 3.040 ... (remaining 72176 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=0.50 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: 0.410 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 26.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 8867 Z= 0.310 Angle : 0.744 18.748 12155 Z= 0.450 Chirality : 0.050 0.258 1387 Planarity : 0.004 0.044 1452 Dihedral : 15.369 89.836 3328 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 999 helix: -0.10 (0.23), residues: 472 sheet: -0.43 (0.47), residues: 97 loop : 0.56 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.019 0.002 HIS C 36 PHE 0.027 0.002 PHE A 652 TYR 0.024 0.002 TYR A 289 ARG 0.009 0.001 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.913 Fit side-chains REVERT: A 160 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7251 (ttpt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.1704 time to fit residues: 190.0671 Evaluate side-chains 130 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 552 ASN A 705 ASN A 790 ASN B 176 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8867 Z= 0.152 Angle : 0.518 7.639 12155 Z= 0.281 Chirality : 0.041 0.188 1387 Planarity : 0.004 0.043 1452 Dihedral : 10.471 73.176 1474 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.02 % Allowed : 9.94 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 999 helix: 0.61 (0.24), residues: 466 sheet: 0.27 (0.52), residues: 86 loop : 0.54 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.013 0.001 HIS C 36 PHE 0.020 0.001 PHE A 652 TYR 0.015 0.001 TYR A 289 ARG 0.004 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.880 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 147 average time/residue: 1.2141 time to fit residues: 190.7747 Evaluate side-chains 132 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 191 GLN A 552 ASN A 724 GLN A 790 ASN B 176 ASN C 34 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8867 Z= 0.170 Angle : 0.501 6.523 12155 Z= 0.272 Chirality : 0.041 0.178 1387 Planarity : 0.004 0.040 1452 Dihedral : 10.402 73.286 1474 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.92 % Allowed : 11.64 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 999 helix: 0.86 (0.24), residues: 469 sheet: 0.33 (0.51), residues: 86 loop : 0.45 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.012 0.001 HIS C 36 PHE 0.019 0.001 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.004 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.973 Fit side-chains REVERT: A 144 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: A 796 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6382 (mt-10) REVERT: A 885 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7438 (mp) outliers start: 17 outliers final: 4 residues processed: 137 average time/residue: 1.1940 time to fit residues: 174.5493 Evaluate side-chains 132 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 177 ASN A 468 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 724 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8867 Z= 0.193 Angle : 0.505 6.911 12155 Z= 0.273 Chirality : 0.041 0.157 1387 Planarity : 0.004 0.040 1452 Dihedral : 10.477 73.275 1474 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.69 % Allowed : 12.66 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 999 helix: 0.93 (0.24), residues: 471 sheet: 0.25 (0.50), residues: 86 loop : 0.35 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.010 0.001 HIS C 36 PHE 0.019 0.001 PHE A 652 TYR 0.018 0.001 TYR A 788 ARG 0.004 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.969 Fit side-chains REVERT: A 136 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6636 (pp20) REVERT: A 796 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6328 (mt-10) REVERT: A 885 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7509 (mp) outliers start: 15 outliers final: 8 residues processed: 136 average time/residue: 1.2037 time to fit residues: 174.8332 Evaluate side-chains 133 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 24 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8867 Z= 0.160 Angle : 0.476 7.148 12155 Z= 0.257 Chirality : 0.040 0.155 1387 Planarity : 0.003 0.039 1452 Dihedral : 10.428 73.356 1474 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.81 % Allowed : 13.56 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 999 helix: 1.06 (0.24), residues: 471 sheet: 0.30 (0.51), residues: 86 loop : 0.33 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.017 0.001 PHE A 652 TYR 0.016 0.001 TYR B 135 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.968 Fit side-chains REVERT: A 167 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5838 (mm-30) REVERT: A 610 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6354 (mt-10) REVERT: A 796 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6248 (mt-10) REVERT: A 885 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7486 (mp) outliers start: 16 outliers final: 5 residues processed: 127 average time/residue: 1.2775 time to fit residues: 172.6048 Evaluate side-chains 125 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8867 Z= 0.239 Angle : 0.522 6.740 12155 Z= 0.282 Chirality : 0.042 0.141 1387 Planarity : 0.004 0.040 1452 Dihedral : 10.542 73.297 1474 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.37 % Allowed : 13.67 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 999 helix: 0.95 (0.24), residues: 471 sheet: 0.26 (0.52), residues: 86 loop : 0.23 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.020 0.002 PHE A 741 TYR 0.018 0.002 TYR A 788 ARG 0.003 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.026 Fit side-chains REVERT: A 197 ARG cc_start: 0.7891 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: A 417 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8276 (tttm) REVERT: A 796 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6309 (mt-10) outliers start: 21 outliers final: 9 residues processed: 126 average time/residue: 1.3076 time to fit residues: 175.3136 Evaluate side-chains 123 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8867 Z= 0.183 Angle : 0.488 6.616 12155 Z= 0.263 Chirality : 0.040 0.150 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.468 73.381 1474 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.69 % Allowed : 14.35 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 999 helix: 1.03 (0.24), residues: 471 sheet: 0.22 (0.53), residues: 86 loop : 0.24 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.018 0.001 PHE A 741 TYR 0.017 0.001 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.888 Fit side-chains REVERT: A 197 ARG cc_start: 0.7864 (ttp-170) cc_final: 0.7546 (ttp-170) REVERT: A 284 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.7005 (t70) REVERT: A 417 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8211 (tttm) REVERT: A 796 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6331 (mt-10) REVERT: A 885 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7580 (mp) outliers start: 15 outliers final: 6 residues processed: 128 average time/residue: 1.3206 time to fit residues: 179.5418 Evaluate side-chains 124 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN B 157 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8867 Z= 0.245 Angle : 0.530 6.861 12155 Z= 0.285 Chirality : 0.042 0.141 1387 Planarity : 0.004 0.039 1452 Dihedral : 10.552 73.352 1474 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.69 % Allowed : 14.80 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 999 helix: 0.95 (0.24), residues: 471 sheet: 0.19 (0.53), residues: 86 loop : 0.18 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.019 0.002 PHE A 741 TYR 0.018 0.002 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.931 Fit side-chains REVERT: A 284 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.7038 (t70) REVERT: A 417 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8211 (tttm) REVERT: A 796 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6344 (mt-10) outliers start: 15 outliers final: 7 residues processed: 124 average time/residue: 1.3404 time to fit residues: 176.5366 Evaluate side-chains 123 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 82 optimal weight: 0.0970 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 177 ASN A 381 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8867 Z= 0.129 Angle : 0.459 6.360 12155 Z= 0.246 Chirality : 0.038 0.154 1387 Planarity : 0.003 0.038 1452 Dihedral : 10.356 73.506 1474 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.24 % Allowed : 15.14 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 999 helix: 1.19 (0.25), residues: 471 sheet: 0.31 (0.55), residues: 86 loop : 0.29 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.015 0.001 PHE A 652 TYR 0.014 0.001 TYR B 135 ARG 0.006 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.999 Fit side-chains REVERT: A 136 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6740 (pp20) REVERT: A 197 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7495 (ttp-170) REVERT: A 796 GLU cc_start: 0.6530 (mm-30) cc_final: 0.6291 (mt-10) outliers start: 11 outliers final: 4 residues processed: 139 average time/residue: 1.3416 time to fit residues: 197.6572 Evaluate side-chains 120 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8867 Z= 0.225 Angle : 0.522 9.651 12155 Z= 0.278 Chirality : 0.041 0.139 1387 Planarity : 0.004 0.038 1452 Dihedral : 10.471 73.382 1474 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.13 % Allowed : 15.14 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 999 helix: 1.03 (0.24), residues: 471 sheet: 0.32 (0.55), residues: 82 loop : 0.26 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.020 0.002 PHE A 741 TYR 0.023 0.002 TYR A 289 ARG 0.005 0.001 ARG A 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.954 Fit side-chains REVERT: A 136 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6660 (pp20) REVERT: A 197 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7630 (ttp-170) REVERT: A 542 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7394 (mmm) REVERT: A 796 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6358 (mt-10) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 1.2983 time to fit residues: 171.6145 Evaluate side-chains 122 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 177 ASN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118576 restraints weight = 8592.049| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.91 r_work: 0.3259 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8867 Z= 0.137 Angle : 0.481 9.805 12155 Z= 0.254 Chirality : 0.039 0.145 1387 Planarity : 0.003 0.038 1452 Dihedral : 10.334 73.494 1474 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.90 % Allowed : 15.93 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 999 helix: 1.18 (0.25), residues: 471 sheet: 0.39 (0.56), residues: 82 loop : 0.30 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.015 0.001 PHE A 652 TYR 0.017 0.001 TYR A 289 ARG 0.006 0.000 ARG A 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3556.75 seconds wall clock time: 62 minutes 49.24 seconds (3769.24 seconds total)