Starting phenix.real_space_refine (version: dev) on Fri May 13 09:48:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yyt_11007/05_2022/6yyt_11007_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yyt_11007/05_2022/6yyt_11007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yyt_11007/05_2022/6yyt_11007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yyt_11007/05_2022/6yyt_11007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yyt_11007/05_2022/6yyt_11007_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yyt_11007/05_2022/6yyt_11007_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.016 sd= 0.974 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 11375 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6880 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 27, 'TRANS': 824, 'PCIS': 1} Chain breaks: 2 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1393 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 179, 'PCIS': 1} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1391 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 179, 'PCIS': 1} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 7, 'rna2p_pur': 1, 'rna3p_pur': 6} Link IDs: {'rna3p': 13} Chain: "Q" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 7, 'rna3p_pur': 7} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 6, 'rna3p_pur': 6} Link IDs: {'rna3p': 11} Chain: "U" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 7, 'rna3p_pur': 7} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1864 SG CYS A 301 92.661 65.587 45.161 1.00 25.99 S ATOM 1905 SG CYS A 306 92.937 64.791 41.187 1.00 25.44 S ATOM 1937 SG CYS A 310 95.767 64.736 44.077 1.00 24.45 S ATOM 3345 SG CYS A 487 75.166 60.156 53.972 1.00 21.81 S ATOM 4598 SG CYS A 645 73.794 60.060 50.132 1.00 27.45 S ATOM 4604 SG CYS A 646 77.157 61.975 51.989 1.00 24.88 S Time building chain proxies: 6.95, per 1000 atoms: 0.61 Number of scatterers: 11375 At special positions: 0 Unit cell: (140.112, 92.574, 127.602, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 77 16.00 P 54 15.00 O 2302 8.00 N 1926 7.00 C 7014 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=0, symmetry=0 Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 57.6% alpha, 10.2% beta 22 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 198 removed outlier: 4.013A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.553A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 3.710A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.251A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.712A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.606A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.685A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.514A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.768A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.542A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.927A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.879A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.869A 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 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.740A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.555A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) 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 789 Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 847 through 852 removed outlier: 4.152A pdb=" N ASP A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 removed outlier: 4.058A pdb=" N ARG A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.555A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.914A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.767A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.322A 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 9 through 29 removed outlier: 3.817A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 98 removed outlier: 3.560A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.700A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.905A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.621A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.230A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.713A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.299A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.601A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 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: 7.051A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.968A 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: 6.040A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.111A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA6, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.735A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3189 1.33 - 1.45: 2214 1.45 - 1.57: 6087 1.57 - 1.69: 102 1.69 - 1.81: 122 Bond restraints: 11714 Sorted by residual: bond pdb=" O3' G T 13 " pdb=" P C T 14 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.93e+00 bond pdb=" O3' A P 17 " pdb=" P G P 18 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.35e+00 bond pdb=" O3' C T 14 " pdb=" P G T 15 " ideal model delta sigma weight residual 1.607 1.574 0.033 1.50e-02 4.44e+03 4.94e+00 bond pdb=" O3' U P 16 " pdb=" P A P 17 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.50e-02 4.44e+03 4.39e+00 bond pdb=" O3' G P 15 " pdb=" P U P 16 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.50e-02 4.44e+03 3.29e+00 ... (remaining 11709 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 563 106.99 - 113.74: 6558 113.74 - 120.50: 4809 120.50 - 127.25: 4009 127.25 - 134.01: 199 Bond angle restraints: 16138 Sorted by residual: angle pdb=" C3' G T 8 " pdb=" C2' G T 8 " pdb=" O2' G T 8 " ideal model delta sigma weight residual 110.70 105.54 5.16 1.50e+00 4.44e-01 1.18e+01 angle pdb=" O3' G P 8 " pdb=" C3' G P 8 " pdb=" C2' G P 8 " ideal model delta sigma weight residual 113.70 109.02 4.68 1.50e+00 4.44e-01 9.72e+00 angle pdb=" C3' A T 11 " pdb=" C2' A T 11 " pdb=" O2' A T 11 " ideal model delta sigma weight residual 110.70 115.34 -4.64 1.50e+00 4.44e-01 9.59e+00 angle pdb=" O3' G T 8 " pdb=" C3' G T 8 " pdb=" C2' G T 8 " ideal model delta sigma weight residual 113.70 109.22 4.48 1.50e+00 4.44e-01 8.90e+00 angle pdb=" O3' G P 18 " pdb=" C3' G P 18 " pdb=" C2' G P 18 " ideal model delta sigma weight residual 109.50 113.86 -4.36 1.50e+00 4.44e-01 8.46e+00 ... (remaining 16133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6111 17.91 - 35.82: 634 35.82 - 53.73: 148 53.73 - 71.63: 14 71.63 - 89.54: 6 Dihedral angle restraints: 6913 sinusoidal: 3056 harmonic: 3857 Sorted by residual: dihedral pdb=" C5' G P 18 " pdb=" C4' G P 18 " pdb=" C3' G P 18 " pdb=" O3' G P 18 " ideal model delta sinusoidal sigma weight residual 147.00 125.28 21.72 1 8.00e+00 1.56e-02 1.07e+01 dihedral pdb=" CB GLU B 48 " pdb=" CG GLU B 48 " pdb=" CD GLU B 48 " pdb=" OE1 GLU B 48 " ideal model delta sinusoidal sigma weight residual 0.00 89.54 -89.54 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 640 " pdb=" CD ARG A 640 " pdb=" NE ARG A 640 " pdb=" CZ ARG A 640 " ideal model delta sinusoidal sigma weight residual 90.00 131.86 -41.86 2 1.50e+01 4.44e-03 9.50e+00 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1588 0.048 - 0.096: 200 0.096 - 0.145: 74 0.145 - 0.193: 11 0.193 - 0.241: 4 Chirality restraints: 1877 Sorted by residual: chirality pdb=" C3' G P 8 " pdb=" C4' G P 8 " pdb=" O3' G P 8 " pdb=" C2' G P 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' G P 18 " pdb=" C4' G P 18 " pdb=" O3' G P 18 " pdb=" C2' G P 18 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2' A T 11 " pdb=" C3' A T 11 " pdb=" O2' A T 11 " pdb=" C1' A T 11 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1874 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G T 13 " -0.019 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 G T 13 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G T 13 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G T 13 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G T 13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G T 13 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G T 13 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G T 13 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G T 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G P 18 " 0.022 2.00e-02 2.50e+03 9.04e-03 2.45e+00 pdb=" N9 G P 18 " -0.017 2.00e-02 2.50e+03 pdb=" C8 G P 18 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G P 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G P 18 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G P 18 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G P 18 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G P 18 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G P 18 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G P 18 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G P 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G P 18 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C P 12 " 0.019 2.00e-02 2.50e+03 9.49e-03 2.03e+00 pdb=" N1 C P 12 " -0.018 2.00e-02 2.50e+03 pdb=" C2 C P 12 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C P 12 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C P 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C P 12 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C P 12 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C P 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C P 12 " -0.007 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2698 2.79 - 3.31: 10547 3.31 - 3.84: 19707 3.84 - 4.37: 23335 4.37 - 4.90: 38279 Nonbonded interactions: 94566 Sorted by model distance: nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.258 2.440 nonbonded pdb=" O GLY A 852 " pdb=" OG1 THR A 853 " model vdw 2.275 2.440 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.347 2.440 nonbonded pdb=" O ASN A 705 " pdb=" OG SER A 709 " model vdw 2.365 2.440 nonbonded pdb=" O ALA A 448 " pdb=" OG SER A 451 " model vdw 2.372 2.440 ... (remaining 94561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 18 or (resid 19 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 191)) } ncs_group { reference = (chain 'P' and resid 7 through 18) selection = (chain 'Q' and resid 7 through 18) selection = chain 'T' selection = (chain 'U' and resid 7 through 18) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 54 5.49 5 S 77 5.16 5 C 7014 2.51 5 N 1926 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 4.150 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.110 Process input model: 40.290 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:14.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.003 0.039 11714 Z= 0.166 Angle : 0.471 5.551 16138 Z= 0.271 Chirality : 0.040 0.241 1877 Planarity : 0.002 0.033 1862 Dihedral : 14.585 89.542 4413 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 (0.21), residues: 1286 helix: -0.06 (0.19), residues: 652 sheet: -0.62 (0.47), residues: 108 loop : -1.31 (0.23), residues: 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.170 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 178 average time/residue: 1.0202 time to fit residues: 200.3010 Evaluate side-chains 150 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.8104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 177 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS A 439 HIS A 468 GLN A 524 GLN A 570 GLN B 88 GLN B 140 ASN D 105 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 11714 Z= 0.272 Angle : 0.520 7.412 16138 Z= 0.266 Chirality : 0.039 0.165 1877 Planarity : 0.004 0.125 1862 Dihedral : 5.866 72.738 2045 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.26 (0.22), residues: 1286 helix: 1.18 (0.20), residues: 660 sheet: -0.44 (0.50), residues: 105 loop : -0.97 (0.24), residues: 521 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.561 Fit side-chains outliers start: 32 outliers final: 13 residues processed: 157 average time/residue: 1.0520 time to fit residues: 182.7788 Evaluate side-chains 146 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.2871 time to fit residues: 3.2229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 909 ASN B 88 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 11714 Z= 0.445 Angle : 0.583 7.452 16138 Z= 0.302 Chirality : 0.042 0.146 1877 Planarity : 0.004 0.079 1862 Dihedral : 6.162 74.936 2045 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 3.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.26 (0.22), residues: 1286 helix: 1.17 (0.20), residues: 670 sheet: -0.58 (0.48), residues: 107 loop : -0.97 (0.24), residues: 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.654 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 162 average time/residue: 1.0251 time to fit residues: 183.6081 Evaluate side-chains 149 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.2012 time to fit residues: 2.6722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 127 optimal weight: 0.0870 chunk 114 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN B 88 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 11714 Z= 0.131 Angle : 0.453 5.952 16138 Z= 0.233 Chirality : 0.036 0.133 1877 Planarity : 0.003 0.058 1862 Dihedral : 6.010 79.932 2045 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.93 (0.23), residues: 1286 helix: 1.70 (0.20), residues: 669 sheet: -0.30 (0.48), residues: 107 loop : -0.60 (0.25), residues: 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.197 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 155 average time/residue: 1.0147 time to fit residues: 173.2574 Evaluate side-chains 150 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.1693 time to fit residues: 2.5553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.2980 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 573 GLN B 88 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 11714 Z= 0.431 Angle : 0.567 7.058 16138 Z= 0.293 Chirality : 0.042 0.175 1877 Planarity : 0.004 0.088 1862 Dihedral : 6.186 78.503 2045 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.66 (0.23), residues: 1286 helix: 1.50 (0.20), residues: 674 sheet: -0.33 (0.51), residues: 97 loop : -0.82 (0.25), residues: 515 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 1.307 Fit side-chains outliers start: 42 outliers final: 23 residues processed: 157 average time/residue: 1.0244 time to fit residues: 177.4559 Evaluate side-chains 148 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.5061 time to fit residues: 4.1470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11714 Z= 0.195 Angle : 0.488 7.746 16138 Z= 0.250 Chirality : 0.037 0.144 1877 Planarity : 0.003 0.075 1862 Dihedral : 6.103 80.870 2045 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 3.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 (0.23), residues: 1286 helix: 1.72 (0.20), residues: 674 sheet: -0.41 (0.48), residues: 107 loop : -0.55 (0.26), residues: 505 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 1.320 Fit side-chains outliers start: 43 outliers final: 25 residues processed: 158 average time/residue: 1.0380 time to fit residues: 180.2778 Evaluate side-chains 150 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.1919 time to fit residues: 2.8622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 71 optimal weight: 0.0050 chunk 127 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 11714 Z= 0.146 Angle : 0.481 10.750 16138 Z= 0.243 Chirality : 0.036 0.138 1877 Planarity : 0.003 0.066 1862 Dihedral : 6.034 82.777 2045 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.26 (0.23), residues: 1286 helix: 1.96 (0.20), residues: 667 sheet: -0.30 (0.48), residues: 107 loop : -0.39 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.409 Fit side-chains outliers start: 38 outliers final: 25 residues processed: 163 average time/residue: 0.9940 time to fit residues: 179.2465 Evaluate side-chains 149 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.1949 time to fit residues: 2.5940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 0.0010 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 40.0000 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11714 Z= 0.196 Angle : 0.491 9.451 16138 Z= 0.251 Chirality : 0.037 0.183 1877 Planarity : 0.003 0.064 1862 Dihedral : 6.039 82.385 2045 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.28 (0.23), residues: 1286 helix: 1.89 (0.20), residues: 672 sheet: -0.32 (0.48), residues: 107 loop : -0.25 (0.27), residues: 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.293 Fit side-chains outliers start: 40 outliers final: 29 residues processed: 158 average time/residue: 1.0551 time to fit residues: 185.1827 Evaluate side-chains 157 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.6646 time to fit residues: 5.5032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 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 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 11714 Z= 0.162 Angle : 0.497 12.201 16138 Z= 0.250 Chirality : 0.037 0.170 1877 Planarity : 0.003 0.063 1862 Dihedral : 6.043 82.871 2045 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.34 (0.24), residues: 1286 helix: 1.93 (0.20), residues: 672 sheet: -0.33 (0.48), residues: 107 loop : -0.20 (0.27), residues: 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.328 Fit side-chains outliers start: 36 outliers final: 26 residues processed: 156 average time/residue: 1.0475 time to fit residues: 180.6590 Evaluate side-chains 152 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 0.5506 time to fit residues: 3.6943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 11714 Z= 0.402 Angle : 0.590 10.645 16138 Z= 0.302 Chirality : 0.042 0.158 1877 Planarity : 0.004 0.063 1862 Dihedral : 6.245 80.158 2045 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.81 (0.23), residues: 1286 helix: 1.45 (0.20), residues: 694 sheet: -0.13 (0.48), residues: 107 loop : -0.58 (0.27), residues: 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.337 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 154 average time/residue: 1.0780 time to fit residues: 182.8089 Evaluate side-chains 146 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.2408 time to fit residues: 2.0354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.140848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098539 restraints weight = 16320.824| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.83 r_work: 0.3332 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 1.65 restraints_weight: 0.2500 r_work: 0.3305 rms_B_bonded: 1.70 restraints_weight: 0.1250 r_work: 0.3290 rms_B_bonded: 1.80 restraints_weight: 0.0625 r_work: 0.3275 rms_B_bonded: 1.94 restraints_weight: 0.0312 r_work: 0.3258 rms_B_bonded: 2.12 restraints_weight: 0.0156 r_work: 0.3241 rms_B_bonded: 2.33 restraints_weight: 0.0078 r_work: 0.3222 rms_B_bonded: 2.58 restraints_weight: 0.0039 r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.0020 r_work: 0.3180 rms_B_bonded: 3.21 restraints_weight: 0.0010 r_work: 0.3156 rms_B_bonded: 3.60 restraints_weight: 0.0005 r_work: 0.3129 rms_B_bonded: 4.04 restraints_weight: 0.0002 r_work: 0.3101 rms_B_bonded: 4.55 restraints_weight: 0.0001 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 11714 Z= 0.155 Angle : 0.527 12.041 16138 Z= 0.264 Chirality : 0.037 0.176 1877 Planarity : 0.003 0.064 1862 Dihedral : 6.125 81.889 2045 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.19 (0.24), residues: 1286 helix: 1.80 (0.20), residues: 675 sheet: -0.38 (0.48), residues: 107 loop : -0.28 (0.27), residues: 504 =============================================================================== Job complete usr+sys time: 3378.29 seconds wall clock time: 61 minutes 19.03 seconds (3679.03 seconds total)