Starting phenix.real_space_refine on Sat Aug 8 19:38:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tb9_41146/08_2026/8tb9_41146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tb9_41146/08_2026/8tb9_41146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2026/8tb9_41146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2026/8tb9_41146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2026/8tb9_41146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2026/8tb9_41146.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 386 5.49 5 S 120 5.16 5 C 17805 2.51 5 N 5548 2.21 5 O 6365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30224 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 196 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 25} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3653 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4580 Classifications: {'peptide': 570} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 538} Chain breaks: 4 Chain: "G" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2930 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3972 Classifications: {'DNA': 193} Link IDs: {'rna3p': 192} Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "O" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3139 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3919 Classifications: {'DNA': 193} Link IDs: {'rna3p': 192} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "W" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "X" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 666 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Y" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1047 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 7.48, per 1000 atoms: 0.25 Number of scatterers: 30224 At special positions: 0 Unit cell: (162.62, 193.64, 180.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 386 15.00 O 6365 8.00 N 5548 7.00 C 17805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 578 " distance=2.02 Simple disulfide: pdb=" SG CYS E 571 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 590 " - pdb=" SG CYS E 593 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 937.3 milliseconds 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5302 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 39 sheets defined 38.8% alpha, 15.2% beta 137 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.780A pdb=" N ILE A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.534A pdb=" N TYR A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'D' and resid 82 through 107 removed outlier: 4.565A pdb=" N LYS D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Proline residue: D 93 - end of helix Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 133 through 146 removed outlier: 4.290A pdb=" N MET D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 244 removed outlier: 3.782A pdb=" N MET D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 471 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 539 through 548 removed outlier: 3.689A pdb=" N GLU D 545 " --> pdb=" O SER D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 579 Processing helix chain 'D' and resid 589 through 603 removed outlier: 3.956A pdb=" N PHE D 603 " --> pdb=" O GLN D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 625 removed outlier: 3.707A pdb=" N VAL D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS D 624 " --> pdb=" O HIS D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 651 removed outlier: 3.564A pdb=" N MET D 637 " --> pdb=" O ASN D 633 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS D 646 " --> pdb=" O ASN D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 removed outlier: 3.940A pdb=" N MET D 663 " --> pdb=" O HIS D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 682 Processing helix chain 'E' and resid 18 through 63 removed outlier: 4.349A pdb=" N LYS E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.723A pdb=" N ARG E 78 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 221 through 231 removed outlier: 3.754A pdb=" N MET E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.920A pdb=" N GLU E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.684A pdb=" N SER E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 278 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 438 through 453 removed outlier: 3.860A pdb=" N GLY E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'E' and resid 471 through 482 Processing helix chain 'E' and resid 500 through 515 removed outlier: 3.894A pdb=" N TRP E 504 " --> pdb=" O LYS E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 576 through 581 Processing helix chain 'E' and resid 609 through 614 removed outlier: 3.665A pdb=" N ARG E 613 " --> pdb=" O CYS E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 665 removed outlier: 3.981A pdb=" N LYS E 665 " --> pdb=" O LYS E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 692 Processing helix chain 'E' and resid 734 through 742 Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 231 through 234 Processing helix chain 'G' and resid 267 through 278 removed outlier: 4.061A pdb=" N MET G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN G 272 " --> pdb=" O LYS G 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 57 Processing helix chain 'I' and resid 63 through 79 removed outlier: 4.309A pdb=" N PHE I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN I 68 " --> pdb=" O LYS I 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG I 69 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.523A pdb=" N VAL I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA I 91 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP I 106 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA I 114 " --> pdb=" O CYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 removed outlier: 3.605A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 removed outlier: 3.502A pdb=" N GLN J 27 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 41 Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.347A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN J 64 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 3.714A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL J 87 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 28 Processing helix chain 'O' and resid 208 through 210 No H-bonds generated for 'chain 'O' and resid 208 through 210' Processing helix chain 'O' and resid 348 through 350 No H-bonds generated for 'chain 'O' and resid 348 through 350' Processing helix chain 'O' and resid 355 through 360 Processing helix chain 'R' and resid 16 through 21 Processing helix chain 'R' and resid 26 through 38 removed outlier: 3.837A pdb=" N ARG R 32 " --> pdb=" O GLY R 28 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 74 removed outlier: 4.385A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 65 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 removed outlier: 3.863A pdb=" N ASP R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 97 removed outlier: 3.525A pdb=" N LYS R 95 " --> pdb=" O GLU R 91 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 116 Processing helix chain 'S' and resid 34 through 46 removed outlier: 3.676A pdb=" N LYS S 43 " --> pdb=" O TYR S 39 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN S 44 " --> pdb=" O LYS S 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 82 removed outlier: 3.501A pdb=" N SER S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN S 64 " --> pdb=" O ASN S 60 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 99 removed outlier: 3.576A pdb=" N ILE S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU S 99 " --> pdb=" O VAL S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 121 removed outlier: 4.189A pdb=" N HIS S 106 " --> pdb=" O GLU S 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 38 removed outlier: 3.625A pdb=" N VAL U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG U 32 " --> pdb=" O GLY U 28 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG U 35 " --> pdb=" O HIS U 31 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN U 38 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.407A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU U 65 " --> pdb=" O GLU U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.559A pdb=" N VAL U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 removed outlier: 4.188A pdb=" N LEU U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 116 Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.758A pdb=" N ASN V 64 " --> pdb=" O ASN V 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE V 67 " --> pdb=" O VAL V 63 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU V 68 " --> pdb=" O ASN V 64 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG V 69 " --> pdb=" O ASP V 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA V 78 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS V 79 " --> pdb=" O SER V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 removed outlier: 3.522A pdb=" N THR V 93 " --> pdb=" O ARG V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 121 Processing helix chain 'W' and resid 44 through 57 removed outlier: 4.054A pdb=" N ARG W 49 " --> pdb=" O THR W 45 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU W 50 " --> pdb=" O VAL W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 79 removed outlier: 3.713A pdb=" N PHE W 67 " --> pdb=" O ARG W 63 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP W 77 " --> pdb=" O GLU W 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 87 through 114 removed outlier: 3.994A pdb=" N ALA W 91 " --> pdb=" O SER W 87 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU W 92 " --> pdb=" O ALA W 88 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS W 110 " --> pdb=" O ASP W 106 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA W 111 " --> pdb=" O THR W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 132 removed outlier: 4.113A pdb=" N ILE W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 29 removed outlier: 3.878A pdb=" N ILE X 29 " --> pdb=" O ILE X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 42 removed outlier: 3.521A pdb=" N ILE X 34 " --> pdb=" O THR X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 77 removed outlier: 4.606A pdb=" N GLU X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR X 54 " --> pdb=" O ILE X 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG X 55 " --> pdb=" O TYR X 51 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN X 64 " --> pdb=" O VAL X 60 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 94 removed outlier: 3.512A pdb=" N TYR X 88 " --> pdb=" O MET X 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 209 removed outlier: 3.812A pdb=" N SER Y 208 " --> pdb=" O CYS Y 204 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 272 No H-bonds generated for 'chain 'Y' and resid 270 through 272' Processing helix chain 'Y' and resid 275 through 281 removed outlier: 4.086A pdb=" N ASP Y 281 " --> pdb=" O ALA Y 277 " (cutoff:3.500A) Processing helix chain 'Y' and resid 282 through 285 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.501A pdb=" N SER A 91 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 230 through 232 removed outlier: 4.356A pdb=" N GLN D 356 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE D 164 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR D 354 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE Y 227 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL Y 226 " --> pdb=" O HIS Y 242 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS Y 242 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA Y 228 " --> pdb=" O LEU Y 240 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL Y 252 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 203 through 211 removed outlier: 3.975A pdb=" N THR D 208 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL D 186 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS D 210 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 184 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 191 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER D 247 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 438 through 443 removed outlier: 3.546A pdb=" N THR D 438 " --> pdb=" O TYR D 434 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE D 429 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL D 489 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN D 431 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ILE D 491 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N LEU D 433 " --> pdb=" O ILE D 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 557 through 559 removed outlier: 3.833A pdb=" N ILE D 525 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 529 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL O 35 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN O 403 " --> pdb=" O ASP O 33 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL O 35 " --> pdb=" O VAL O 401 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL O 401 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR O 37 " --> pdb=" O MET O 399 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET O 399 " --> pdb=" O THR O 37 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE O 398 " --> pdb=" O SER O 394 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP O 402 " --> pdb=" O ILE O 390 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET O 404 " --> pdb=" O TRP O 388 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TRP O 388 " --> pdb=" O MET O 404 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL O 389 " --> pdb=" O ASN O 383 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN O 383 " --> pdb=" O VAL O 389 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 566 through 567 Processing sheet with id=AA7, first strand: chain 'E' and resid 94 through 97 removed outlier: 3.674A pdb=" N GLN E 94 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 114 through 115 removed outlier: 5.478A pdb=" N SER E 114 " --> pdb=" O GLY E 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 119 through 121 removed outlier: 6.406A pdb=" N PHE E 120 " --> pdb=" O ILE E 650 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N SER E 652 " --> pdb=" O PHE E 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 285 through 286 Processing sheet with id=AB2, first strand: chain 'E' and resid 619 through 623 Processing sheet with id=AB3, first strand: chain 'E' and resid 693 through 694 removed outlier: 6.262A pdb=" N ASN E 693 " --> pdb=" O PHE E 729 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 700 through 707 Processing sheet with id=AB5, first strand: chain 'G' and resid 82 through 86 removed outlier: 6.753A pdb=" N ARG G 436 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN G 415 " --> pdb=" O VAL G 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 99 through 101 removed outlier: 3.707A pdb=" N LEU G 123 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN G 136 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU G 125 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU G 134 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 147 through 154 removed outlier: 7.112A pdb=" N ILE G 172 " --> pdb=" O HIS G 185 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N HIS G 185 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE G 174 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE G 183 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 193 through 198 removed outlier: 6.372A pdb=" N VAL G 209 " --> pdb=" O ASN G 194 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU G 196 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G 207 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE G 198 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU G 205 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU G 206 " --> pdb=" O TRP G 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP G 218 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER G 208 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG G 216 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU G 215 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE G 228 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU G 217 " --> pdb=" O VAL G 226 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ILE G 294 " --> pdb=" O VAL G 226 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE G 228 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 239 through 244 Processing sheet with id=AC1, first strand: chain 'G' and resid 309 through 311 removed outlier: 3.505A pdb=" N CYS G 311 " --> pdb=" O LYS G 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 309 through 311 removed outlier: 3.505A pdb=" N CYS G 311 " --> pdb=" O LYS G 322 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 369 through 370 removed outlier: 3.590A pdb=" N ALA G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.181A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AC6, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.615A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'O' and resid 47 through 49 removed outlier: 3.514A pdb=" N GLN O 48 " --> pdb=" O VAL O 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN O 77 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER O 83 " --> pdb=" O ILE O 117 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE O 117 " --> pdb=" O SER O 83 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN O 85 " --> pdb=" O ILE O 115 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE O 115 " --> pdb=" O GLN O 85 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 129 through 133 removed outlier: 3.547A pdb=" N ARG O 129 " --> pdb=" O LYS O 143 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE O 139 " --> pdb=" O MET O 133 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 172 through 173 removed outlier: 6.693A pdb=" N ARG O 172 " --> pdb=" O VAL O 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'O' and resid 183 through 185 removed outlier: 3.583A pdb=" N LEU O 193 " --> pdb=" O TRP O 205 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 230 through 235 removed outlier: 4.329A pdb=" N ALA O 247 " --> pdb=" O LYS O 251 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS O 251 " --> pdb=" O ALA O 247 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 279 through 281 removed outlier: 4.336A pdb=" N HIS O 311 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 320 through 325 removed outlier: 3.794A pdb=" N GLN O 322 " --> pdb=" O SER O 336 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP O 346 " --> pdb=" O LEU O 366 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU O 366 " --> pdb=" O ASP O 346 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.131A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AD7, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.233A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AD9, first strand: chain 'U' and resid 101 through 102 removed outlier: 7.067A pdb=" N THR U 101 " --> pdb=" O TYR X 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'W' and resid 83 through 84 removed outlier: 7.235A pdb=" N ARG W 83 " --> pdb=" O VAL X 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'W' and resid 118 through 119 removed outlier: 3.676A pdb=" N ILE W 119 " --> pdb=" O ARG X 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'Y' and resid 219 through 222 878 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 400 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8028 1.33 - 1.46: 8141 1.46 - 1.58: 14531 1.58 - 1.70: 771 1.70 - 1.82: 174 Bond restraints: 31645 Sorted by residual: bond pdb=" C3' DA H 42 " pdb=" C2' DA H 42 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DG H 192 " pdb=" C2' DG H 192 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG H 136 " pdb=" C2' DG H 136 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC T 58 " pdb=" C2' DC T 58 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA T 192 " pdb=" C2' DA T 192 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 ... (remaining 31640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 43653 3.89 - 7.78: 164 7.78 - 11.67: 527 11.67 - 15.57: 45 15.57 - 19.46: 14 Bond angle restraints: 44403 Sorted by residual: angle pdb=" O3' DC T 67 " pdb=" P DC T 68 " pdb=" OP1 DC T 68 " ideal model delta sigma weight residual 108.00 127.46 -19.46 3.00e+00 1.11e-01 4.21e+01 angle pdb=" O3' DA T 109 " pdb=" P DC T 110 " pdb=" OP1 DC T 110 " ideal model delta sigma weight residual 108.00 126.87 -18.87 3.00e+00 1.11e-01 3.96e+01 angle pdb=" O3' DC H 59 " pdb=" P DA H 60 " pdb=" OP1 DA H 60 " ideal model delta sigma weight residual 108.00 126.28 -18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" O3' DC T 104 " pdb=" P DA T 105 " pdb=" OP1 DA T 105 " ideal model delta sigma weight residual 108.00 126.23 -18.23 3.00e+00 1.11e-01 3.69e+01 angle pdb=" O3' DC T 82 " pdb=" P DA T 83 " pdb=" OP1 DA T 83 " ideal model delta sigma weight residual 108.00 126.15 -18.15 3.00e+00 1.11e-01 3.66e+01 ... (remaining 44398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 16106 35.66 - 71.33: 1891 71.33 - 106.99: 66 106.99 - 142.65: 3 142.65 - 178.31: 22 Dihedral angle restraints: 18088 sinusoidal: 9936 harmonic: 8152 Sorted by residual: dihedral pdb=" CB CYS E 590 " pdb=" SG CYS E 590 " pdb=" SG CYS E 593 " pdb=" CB CYS E 593 " ideal model delta sinusoidal sigma weight residual 93.00 164.36 -71.36 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA GLY S 101 " pdb=" C GLY S 101 " pdb=" N GLU S 102 " pdb=" CA GLU S 102 " ideal model delta harmonic sigma weight residual 180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA GLY E 564 " pdb=" C GLY E 564 " pdb=" N CYS E 565 " pdb=" CA CYS E 565 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 18085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4558 0.126 - 0.251: 57 0.251 - 0.377: 78 0.377 - 0.502: 217 0.502 - 0.628: 18 Chirality restraints: 4928 Sorted by residual: chirality pdb=" P DC T 68 " pdb=" OP1 DC T 68 " pdb=" OP2 DC T 68 " pdb=" O5' DC T 68 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.86e+00 chirality pdb=" P DC T 110 " pdb=" OP1 DC T 110 " pdb=" OP2 DC T 110 " pdb=" O5' DC T 110 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" P DA T 83 " pdb=" OP1 DA T 83 " pdb=" OP2 DA T 83 " pdb=" O5' DA T 83 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.12e+00 ... (remaining 4925 not shown) Planarity restraints: 4342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 326 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO E 327 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO E 327 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO E 327 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 79 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.34e+00 pdb=" N PRO R 80 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 81 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP I 81 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP I 81 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU I 82 " -0.010 2.00e-02 2.50e+03 ... (remaining 4339 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1286 2.66 - 3.22: 31507 3.22 - 3.78: 57373 3.78 - 4.34: 72990 4.34 - 4.90: 104236 Nonbonded interactions: 267392 Sorted by model distance: nonbonded pdb=" O TYR R 39 " pdb=" OG SER S 75 " model vdw 2.104 3.040 nonbonded pdb=" OG SER A 91 " pdb=" OP1 DG T 116 " model vdw 2.121 3.040 nonbonded pdb=" O TRP O 24 " pdb=" OG1 THR O 28 " model vdw 2.151 3.040 nonbonded pdb=" OG SER D 568 " pdb=" OE1 GLU D 584 " model vdw 2.165 3.040 nonbonded pdb=" O2 DC H 184 " pdb=" N2 DG T 43 " model vdw 2.169 3.120 ... (remaining 267387 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 Found NCS groups: ncs_group { reference = (chain 'I' and resid 37 through 135) selection = chain 'W' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'X' and resid 20 through 102) } ncs_group { reference = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) selection = chain 'U' } ncs_group { reference = (chain 'S' and resid 28 through 122) selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.730 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 0.096 31648 Z= 0.424 Angle : 1.442 19.458 44409 Z= 0.680 Chirality : 0.112 0.628 4928 Planarity : 0.004 0.127 4342 Dihedral : 24.498 178.314 12777 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 0.25 % Allowed : 19.05 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 2735 helix: 0.03 (0.16), residues: 924 sheet: -1.17 (0.25), residues: 405 loop : -0.89 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 719 TYR 0.017 0.001 TYR A 27 PHE 0.018 0.001 PHE G 296 TRP 0.012 0.001 TRP O 235 HIS 0.011 0.001 HIS Y 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.42 (31645) covalent geometry : angle 1.44199 / 0.68 (44403) SS BOND : bond 0.01215 / 0.62 ( 3) SS BOND : angle 3.11957 / 1.61 ( 6) hydrogen bonds : bond 0.31906 / 21.49 ( 1181) hydrogen bonds : angle 9.33102 / 6.43 ( 2905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 681 ASP cc_start: 0.9179 (p0) cc_final: 0.8485 (t0) REVERT: G 379 LEU cc_start: 0.9050 (tp) cc_final: 0.8698 (mp) REVERT: O 36 MET cc_start: 0.8370 (mmp) cc_final: 0.6401 (tmm) REVERT: O 133 MET cc_start: 0.8585 (tmm) cc_final: 0.7663 (tmm) outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.1897 time to fit residues: 39.7903 Evaluate side-chains 120 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain Y residue 254 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0570 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 221 GLN D 517 ASN E 273 GLN E 315 ASN E 520 ASN E 526 GLN E 618 HIS E 693 ASN G 157 ASN G 181 GLN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 HIS G 292 GLN G 382 GLN ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 HIS ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 ASN ** O 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 ASN O 385 ASN R 31 HIS R 94 ASN R 112 GLN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 ASN U 112 GLN V 44 GLN ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN Y 187 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.046805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.029709 restraints weight = 335813.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.030341 restraints weight = 190030.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.030770 restraints weight = 132213.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.031012 restraints weight = 107198.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.031190 restraints weight = 95948.893| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 31648 Z= 0.210 Angle : 0.757 9.367 44409 Z= 0.420 Chirality : 0.049 0.351 4928 Planarity : 0.005 0.126 4342 Dihedral : 28.573 178.011 7243 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.84 % Allowed : 17.40 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 2735 helix: 0.14 (0.15), residues: 980 sheet: -1.50 (0.23), residues: 398 loop : -1.02 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 658 TYR 0.016 0.002 TYR G 244 PHE 0.025 0.002 PHE W 104 TRP 0.013 0.002 TRP O 255 HIS 0.008 0.001 HIS Y 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.21 (31645) covalent geometry : angle 0.75653 / 0.42 (44403) SS BOND : bond 0.01434 / 0.74 ( 3) SS BOND : angle 2.59121 / 1.39 ( 6) hydrogen bonds : bond 0.12290 / 8.44 ( 1181) hydrogen bonds : angle 6.13902 / 4.21 ( 2905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 122 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 632 MET cc_start: 0.9361 (tpp) cc_final: 0.9157 (mpp) REVERT: E 41 MET cc_start: 0.9489 (mpp) cc_final: 0.9269 (mpp) REVERT: E 111 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: E 681 ASP cc_start: 0.9212 (p0) cc_final: 0.8783 (t0) REVERT: G 213 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8178 (m90) REVERT: O 36 MET cc_start: 0.8640 (mmp) cc_final: 0.6645 (tmm) REVERT: O 383 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6379 (p0) REVERT: W 106 ASP cc_start: 0.9195 (m-30) cc_final: 0.8987 (m-30) REVERT: X 92 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8932 (ttp80) REVERT: Y 288 MET cc_start: 0.8616 (ttt) cc_final: 0.8349 (tmm) outliers start: 69 outliers final: 34 residues processed: 175 average time/residue: 0.1687 time to fit residues: 48.6575 Evaluate side-chains 152 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 578 CYS Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 297 THR Chi-restraints excluded: chain O residue 383 ASN Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 90 MET Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 92 ARG Chi-restraints excluded: chain Y residue 242 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 290 optimal weight: 6.9990 chunk 307 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 150 optimal weight: 40.0000 chunk 47 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 chunk 298 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 163 optimal weight: 50.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN D 620 HIS D 624 HIS ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 343 ASN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 HIS X 75 HIS Y 187 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.047591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.030148 restraints weight = 327994.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.030868 restraints weight = 183370.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.031311 restraints weight = 129593.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.031629 restraints weight = 106593.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.031791 restraints weight = 93680.835| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 31648 Z= 0.154 Angle : 0.689 9.694 44409 Z= 0.382 Chirality : 0.047 0.346 4928 Planarity : 0.005 0.126 4342 Dihedral : 28.616 179.537 7236 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.90 % Favored : 95.03 % Rotamer: Outliers : 2.34 % Allowed : 18.10 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 2735 helix: 0.33 (0.16), residues: 988 sheet: -1.53 (0.24), residues: 374 loop : -0.97 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 522 TYR 0.014 0.001 TYR G 244 PHE 0.022 0.001 PHE E 32 TRP 0.018 0.001 TRP E 437 HIS 0.035 0.001 HIS G 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (31645) covalent geometry : angle 0.68856 / 0.38 (44403) SS BOND : bond 0.00754 / 0.38 ( 3) SS BOND : angle 2.20720 / 1.22 ( 6) hydrogen bonds : bond 0.11323 / 7.75 ( 1181) hydrogen bonds : angle 5.52158 / 3.80 ( 2905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 MET cc_start: 0.7587 (tpt) cc_final: 0.7296 (tpt) REVERT: E 681 ASP cc_start: 0.9235 (p0) cc_final: 0.8751 (t0) REVERT: G 379 LEU cc_start: 0.9454 (tp) cc_final: 0.8913 (mp) REVERT: I 67 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8184 (t80) REVERT: J 84 MET cc_start: 0.9087 (mpp) cc_final: 0.8857 (mpp) REVERT: O 36 MET cc_start: 0.8564 (mmp) cc_final: 0.6615 (tmm) REVERT: O 37 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8741 (p) REVERT: O 133 MET cc_start: 0.8731 (tmm) cc_final: 0.7708 (tmm) REVERT: O 404 MET cc_start: 0.8521 (pmm) cc_final: 0.8166 (pmm) REVERT: S 81 ASN cc_start: 0.9261 (m-40) cc_final: 0.8887 (p0) REVERT: W 104 PHE cc_start: 0.9163 (m-80) cc_final: 0.8869 (m-80) REVERT: W 106 ASP cc_start: 0.9192 (m-30) cc_final: 0.8903 (m-30) REVERT: W 120 MET cc_start: 0.8487 (mpp) cc_final: 0.8024 (mpp) REVERT: X 92 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.9069 (ttp80) outliers start: 57 outliers final: 30 residues processed: 173 average time/residue: 0.1810 time to fit residues: 52.0846 Evaluate side-chains 151 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 599 TRP Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 92 ARG Chi-restraints excluded: chain Y residue 194 THR Chi-restraints excluded: chain Y residue 242 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 123 optimal weight: 20.0000 chunk 147 optimal weight: 50.0000 chunk 68 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 305 optimal weight: 30.0000 chunk 132 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 150 optimal weight: 40.0000 chunk 42 optimal weight: 3.9990 chunk 252 optimal weight: 40.0000 chunk 171 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 HIS ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 GLN J 93 GLN O 383 ASN O 410 ASN R 89 ASN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Y 268 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.046303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.029104 restraints weight = 336774.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.029798 restraints weight = 189206.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.030271 restraints weight = 134220.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.030503 restraints weight = 109234.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.030618 restraints weight = 97874.965| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 31648 Z= 0.215 Angle : 0.714 10.695 44409 Z= 0.394 Chirality : 0.047 0.381 4928 Planarity : 0.005 0.128 4342 Dihedral : 28.657 179.214 7236 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 3.17 % Allowed : 18.43 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 2735 helix: 0.28 (0.16), residues: 985 sheet: -1.61 (0.24), residues: 381 loop : -0.99 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 475 TYR 0.016 0.002 TYR V 37 PHE 0.021 0.002 PHE D 476 TRP 0.011 0.002 TRP E 113 HIS 0.007 0.001 HIS U 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 (31645) covalent geometry : angle 0.71357 / 0.39 (44403) SS BOND : bond 0.01287 / 0.65 ( 3) SS BOND : angle 2.26805 / 1.13 ( 6) hydrogen bonds : bond 0.10529 / 7.08 ( 1181) hydrogen bonds : angle 5.49843 / 3.79 ( 2905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 114 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7217 (tpt) REVERT: E 705 MET cc_start: 0.8657 (tpt) cc_final: 0.8300 (mmm) REVERT: E 706 MET cc_start: 0.9222 (tpp) cc_final: 0.8964 (tpp) REVERT: G 213 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8090 (m170) REVERT: G 379 LEU cc_start: 0.9528 (tp) cc_final: 0.9155 (mp) REVERT: I 67 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8212 (t80) REVERT: J 84 MET cc_start: 0.9160 (mpp) cc_final: 0.8953 (mpp) REVERT: O 36 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.6726 (tmm) REVERT: O 37 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8769 (p) REVERT: O 383 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.7029 (p0) REVERT: O 404 MET cc_start: 0.8549 (pmm) cc_final: 0.8276 (pmm) REVERT: S 81 ASN cc_start: 0.9264 (m-40) cc_final: 0.8876 (p0) REVERT: W 106 ASP cc_start: 0.9271 (m-30) cc_final: 0.9003 (m-30) REVERT: X 92 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.9160 (ttp80) REVERT: Y 288 MET cc_start: 0.8796 (ttt) cc_final: 0.8473 (ttt) outliers start: 77 outliers final: 46 residues processed: 177 average time/residue: 0.1689 time to fit residues: 48.8405 Evaluate side-chains 162 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain E residue 599 TRP Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain O residue 383 ASN Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 92 ARG Chi-restraints excluded: chain Y residue 194 THR Chi-restraints excluded: chain Y residue 242 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 241 optimal weight: 3.9990 chunk 23 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 254 optimal weight: 30.0000 chunk 180 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 HIS ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 ASN ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.046997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.029689 restraints weight = 333421.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.030326 restraints weight = 186239.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.030825 restraints weight = 131191.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.031099 restraints weight = 106485.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.031244 restraints weight = 94494.900| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 31648 Z= 0.156 Angle : 0.673 10.553 44409 Z= 0.373 Chirality : 0.046 0.388 4928 Planarity : 0.005 0.127 4342 Dihedral : 28.647 178.978 7236 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 2.92 % Allowed : 18.72 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2735 helix: 0.46 (0.16), residues: 985 sheet: -1.44 (0.24), residues: 382 loop : -0.94 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 475 TYR 0.012 0.001 TYR G 244 PHE 0.021 0.001 PHE E 32 TRP 0.014 0.001 TRP E 60 HIS 0.021 0.001 HIS G 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (31645) covalent geometry : angle 0.67307 / 0.37 (44403) SS BOND : bond 0.00862 / 0.44 ( 3) SS BOND : angle 2.08389 / 1.11 ( 6) hydrogen bonds : bond 0.10285 / 7.01 ( 1181) hydrogen bonds : angle 5.24420 / 3.62 ( 2905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 120 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7567 (m) REVERT: A 80 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7218 (tt) REVERT: E 565 CYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6238 (t) REVERT: I 67 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8214 (t80) REVERT: J 84 MET cc_start: 0.9152 (mpp) cc_final: 0.8916 (mpp) REVERT: O 36 MET cc_start: 0.8555 (mmp) cc_final: 0.6628 (tmm) REVERT: O 37 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8680 (p) REVERT: O 133 MET cc_start: 0.8772 (tmm) cc_final: 0.7713 (tmm) REVERT: S 81 ASN cc_start: 0.9178 (m-40) cc_final: 0.8866 (p0) REVERT: W 104 PHE cc_start: 0.9188 (m-10) cc_final: 0.8788 (m-80) REVERT: W 106 ASP cc_start: 0.9244 (m-30) cc_final: 0.8968 (m-30) REVERT: X 92 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.9140 (ttp80) REVERT: X 98 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7733 (m-10) outliers start: 71 outliers final: 40 residues processed: 179 average time/residue: 0.1900 time to fit residues: 55.0751 Evaluate side-chains 158 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 92 ARG Chi-restraints excluded: chain X residue 98 TYR Chi-restraints excluded: chain Y residue 194 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 25 optimal weight: 5.9990 chunk 146 optimal weight: 50.0000 chunk 83 optimal weight: 0.0670 chunk 162 optimal weight: 30.0000 chunk 201 optimal weight: 20.0000 chunk 268 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.046909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.029627 restraints weight = 332186.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.030327 restraints weight = 183176.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.030818 restraints weight = 129456.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.031073 restraints weight = 105085.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.031269 restraints weight = 93900.228| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 31648 Z= 0.159 Angle : 0.672 16.058 44409 Z= 0.370 Chirality : 0.046 0.483 4928 Planarity : 0.005 0.128 4342 Dihedral : 28.586 179.582 7236 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.48 % Rotamer: Outliers : 3.04 % Allowed : 18.84 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2735 helix: 0.53 (0.16), residues: 982 sheet: -1.41 (0.24), residues: 387 loop : -0.92 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 509 TYR 0.031 0.001 TYR G 148 PHE 0.019 0.001 PHE E 32 TRP 0.013 0.001 TRP E 60 HIS 0.005 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (31645) covalent geometry : angle 0.67168 / 0.37 (44403) SS BOND : bond 0.00849 / 0.43 ( 3) SS BOND : angle 2.09070 / 1.10 ( 6) hydrogen bonds : bond 0.10064 / 6.84 ( 1181) hydrogen bonds : angle 5.10771 / 3.54 ( 2905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 118 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7504 (m) REVERT: A 80 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7220 (tt) REVERT: D 118 MET cc_start: 0.7507 (tpt) cc_final: 0.7213 (tpt) REVERT: E 565 CYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6282 (t) REVERT: E 705 MET cc_start: 0.8704 (tpt) cc_final: 0.8153 (tmm) REVERT: G 415 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: I 67 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8152 (t80) REVERT: O 36 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.6651 (tmm) REVERT: O 37 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8492 (p) REVERT: R 78 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9031 (tp) REVERT: S 68 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8214 (tp30) REVERT: S 81 ASN cc_start: 0.9099 (m-40) cc_final: 0.8866 (p0) REVERT: W 104 PHE cc_start: 0.9202 (m-10) cc_final: 0.8858 (m-80) REVERT: W 106 ASP cc_start: 0.9246 (m-30) cc_final: 0.8973 (m-30) REVERT: X 98 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7597 (m-80) outliers start: 74 outliers final: 48 residues processed: 180 average time/residue: 0.1928 time to fit residues: 57.3595 Evaluate side-chains 168 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 599 TRP Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 415 GLN Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Chi-restraints excluded: chain Y residue 194 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 196 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 283 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 157 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 HIS ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.046202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.029056 restraints weight = 336582.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.029754 restraints weight = 187305.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.030180 restraints weight = 132523.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.030478 restraints weight = 109487.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.030630 restraints weight = 96588.217| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 31648 Z= 0.206 Angle : 0.704 12.658 44409 Z= 0.385 Chirality : 0.046 0.413 4928 Planarity : 0.005 0.128 4342 Dihedral : 28.614 178.882 7236 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 3.09 % Allowed : 19.25 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.16), residues: 2735 helix: 0.47 (0.16), residues: 980 sheet: -1.41 (0.24), residues: 383 loop : -1.00 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 475 TYR 0.022 0.002 TYR G 148 PHE 0.019 0.001 PHE E 32 TRP 0.012 0.002 TRP E 113 HIS 0.008 0.001 HIS R 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.21 (31645) covalent geometry : angle 0.70326 / 0.39 (44403) SS BOND : bond 0.01115 / 0.56 ( 3) SS BOND : angle 2.26197 / 1.14 ( 6) hydrogen bonds : bond 0.09952 / 6.72 ( 1181) hydrogen bonds : angle 5.22333 / 3.61 ( 2905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 112 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7591 (m) REVERT: A 80 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7179 (tt) REVERT: E 41 MET cc_start: 0.9400 (mmm) cc_final: 0.9158 (mpp) REVERT: E 110 MET cc_start: 0.8718 (ppp) cc_final: 0.8444 (tmm) REVERT: E 565 CYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6361 (t) REVERT: G 213 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8674 (m170) REVERT: G 379 LEU cc_start: 0.9537 (tp) cc_final: 0.9010 (pp) REVERT: G 415 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: I 67 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8226 (t80) REVERT: S 81 ASN cc_start: 0.9105 (m-40) cc_final: 0.8838 (p0) REVERT: W 104 PHE cc_start: 0.9266 (m-10) cc_final: 0.8915 (m-80) REVERT: W 106 ASP cc_start: 0.9297 (m-30) cc_final: 0.9039 (m-30) REVERT: X 63 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.9028 (pm20) REVERT: X 98 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: Y 288 MET cc_start: 0.8776 (ttt) cc_final: 0.8555 (ttt) outliers start: 75 outliers final: 56 residues processed: 173 average time/residue: 0.1845 time to fit residues: 53.8397 Evaluate side-chains 175 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 111 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 663 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 599 TRP Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 415 GLN Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 63 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Chi-restraints excluded: chain Y residue 242 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 112 optimal weight: 9.9990 chunk 208 optimal weight: 0.4980 chunk 264 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 146 optimal weight: 50.0000 chunk 251 optimal weight: 30.0000 chunk 104 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.046604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.029532 restraints weight = 331583.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.030077 restraints weight = 187620.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.030516 restraints weight = 130355.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.030812 restraints weight = 107111.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.030969 restraints weight = 94425.530| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 31648 Z= 0.161 Angle : 0.682 15.104 44409 Z= 0.372 Chirality : 0.046 0.467 4928 Planarity : 0.004 0.128 4342 Dihedral : 28.608 179.730 7236 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 2.92 % Allowed : 19.87 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2735 helix: 0.54 (0.16), residues: 978 sheet: -1.41 (0.25), residues: 377 loop : -0.99 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 475 TYR 0.017 0.001 TYR G 148 PHE 0.019 0.001 PHE E 32 TRP 0.013 0.001 TRP E 60 HIS 0.009 0.001 HIS Y 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (31645) covalent geometry : angle 0.68115 / 0.37 (44403) SS BOND : bond 0.00819 / 0.42 ( 3) SS BOND : angle 2.20953 / 1.18 ( 6) hydrogen bonds : bond 0.09902 / 6.72 ( 1181) hydrogen bonds : angle 5.05676 / 3.50 ( 2905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 115 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 MET cc_start: 0.7494 (tpt) cc_final: 0.7191 (tpt) REVERT: D 614 MET cc_start: 0.9563 (pmm) cc_final: 0.9360 (pmm) REVERT: E 41 MET cc_start: 0.9392 (mmm) cc_final: 0.9142 (mpp) REVERT: E 110 MET cc_start: 0.8711 (ppp) cc_final: 0.8461 (tmm) REVERT: E 565 CYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6385 (t) REVERT: G 213 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8598 (m170) REVERT: G 415 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: I 67 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8158 (t80) REVERT: I 103 LEU cc_start: 0.9562 (tp) cc_final: 0.9350 (tp) REVERT: O 36 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.6887 (tpp) REVERT: R 110 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.9151 (m110) REVERT: S 81 ASN cc_start: 0.9054 (m-40) cc_final: 0.8838 (p0) REVERT: W 104 PHE cc_start: 0.9248 (m-10) cc_final: 0.8892 (m-80) REVERT: W 106 ASP cc_start: 0.9268 (m-30) cc_final: 0.9001 (m-30) REVERT: W 120 MET cc_start: 0.8377 (mpp) cc_final: 0.8131 (mpp) REVERT: X 98 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7564 (m-80) outliers start: 71 outliers final: 52 residues processed: 170 average time/residue: 0.1827 time to fit residues: 52.2731 Evaluate side-chains 172 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 113 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 567 CYS Chi-restraints excluded: chain E residue 599 TRP Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 415 GLN Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 23 optimal weight: 50.0000 chunk 232 optimal weight: 3.9990 chunk 162 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 290 optimal weight: 8.9990 chunk 305 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.045917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.028757 restraints weight = 336232.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.029493 restraints weight = 189216.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.029904 restraints weight = 134439.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.030192 restraints weight = 111294.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.030339 restraints weight = 98118.149| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 31648 Z= 0.210 Angle : 0.711 14.501 44409 Z= 0.388 Chirality : 0.046 0.417 4928 Planarity : 0.005 0.129 4342 Dihedral : 28.642 178.653 7236 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 2.59 % Allowed : 20.24 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.16), residues: 2735 helix: 0.40 (0.16), residues: 980 sheet: -1.36 (0.25), residues: 379 loop : -0.98 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 516 TYR 0.015 0.002 TYR S 37 PHE 0.019 0.002 PHE E 32 TRP 0.015 0.002 TRP G 218 HIS 0.008 0.001 HIS G 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 (31645) covalent geometry : angle 0.71016 / 0.39 (44403) SS BOND : bond 0.01112 / 0.56 ( 3) SS BOND : angle 2.32198 / 1.21 ( 6) hydrogen bonds : bond 0.09899 / 6.66 ( 1181) hydrogen bonds : angle 5.21225 / 3.60 ( 2905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 113 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 MET cc_start: 0.7569 (tpt) cc_final: 0.7251 (tpt) REVERT: D 614 MET cc_start: 0.9557 (pmm) cc_final: 0.9166 (pmm) REVERT: E 110 MET cc_start: 0.8705 (ppp) cc_final: 0.8485 (tmm) REVERT: E 565 CYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6435 (t) REVERT: G 213 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8414 (m170) REVERT: G 415 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: I 67 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8233 (t80) REVERT: I 103 LEU cc_start: 0.9559 (tp) cc_final: 0.9341 (tp) REVERT: O 36 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: R 110 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9143 (m110) REVERT: S 81 ASN cc_start: 0.9078 (m-40) cc_final: 0.8838 (p0) REVERT: W 104 PHE cc_start: 0.9282 (m-10) cc_final: 0.8927 (m-80) REVERT: W 106 ASP cc_start: 0.9298 (m-30) cc_final: 0.9042 (m-30) REVERT: X 98 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: Y 288 MET cc_start: 0.8556 (ttt) cc_final: 0.8307 (tmm) outliers start: 63 outliers final: 53 residues processed: 162 average time/residue: 0.1866 time to fit residues: 50.7450 Evaluate side-chains 173 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 567 CYS Chi-restraints excluded: chain E residue 599 TRP Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 415 GLN Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 93 LEU Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Chi-restraints excluded: chain Y residue 242 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 59 optimal weight: 50.0000 chunk 118 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 153 optimal weight: 40.0000 chunk 275 optimal weight: 3.9990 chunk 282 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 260 optimal weight: 40.0000 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.045688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.028803 restraints weight = 338225.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.029330 restraints weight = 191092.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.029764 restraints weight = 135136.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.030000 restraints weight = 110028.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.030179 restraints weight = 98534.634| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 31648 Z= 0.205 Angle : 0.721 17.007 44409 Z= 0.392 Chirality : 0.047 0.476 4928 Planarity : 0.005 0.128 4342 Dihedral : 28.716 179.006 7236 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Rotamer: Outliers : 2.47 % Allowed : 20.65 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2735 helix: 0.34 (0.16), residues: 986 sheet: -1.39 (0.25), residues: 392 loop : -1.01 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 475 TYR 0.014 0.002 TYR S 37 PHE 0.020 0.002 PHE E 120 TRP 0.013 0.002 TRP G 218 HIS 0.010 0.001 HIS E 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 (31645) covalent geometry : angle 0.72054 / 0.39 (44403) SS BOND : bond 0.01079 / 0.54 ( 3) SS BOND : angle 2.46189 / 1.36 ( 6) hydrogen bonds : bond 0.09891 / 6.67 ( 1181) hydrogen bonds : angle 5.21076 / 3.60 ( 2905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 MET cc_start: 0.7866 (tpt) cc_final: 0.7573 (tpt) REVERT: D 614 MET cc_start: 0.9588 (pmm) cc_final: 0.9370 (pmm) REVERT: E 565 CYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6629 (t) REVERT: E 706 MET cc_start: 0.9222 (tpp) cc_final: 0.9000 (tpp) REVERT: G 213 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8344 (m-70) REVERT: G 379 LEU cc_start: 0.9464 (tp) cc_final: 0.9208 (tp) REVERT: I 67 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8220 (t80) REVERT: I 103 LEU cc_start: 0.9550 (tp) cc_final: 0.9322 (tp) REVERT: O 36 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: O 140 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9212 (mp) REVERT: R 110 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.9125 (m110) REVERT: S 81 ASN cc_start: 0.9087 (m-40) cc_final: 0.8824 (p0) REVERT: V 73 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9089 (mm-30) REVERT: W 104 PHE cc_start: 0.9281 (m-10) cc_final: 0.8889 (m-80) REVERT: W 106 ASP cc_start: 0.9309 (m-30) cc_final: 0.9053 (m-30) REVERT: X 63 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8997 (pm20) REVERT: X 98 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: Y 288 MET cc_start: 0.8707 (ttt) cc_final: 0.8308 (tmm) outliers start: 60 outliers final: 46 residues processed: 161 average time/residue: 0.1817 time to fit residues: 48.5853 Evaluate side-chains 163 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 108 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 279 HIS Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 567 CYS Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 352 ILE Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 73 GLU Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.046503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.029355 restraints weight = 334617.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.030016 restraints weight = 186158.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.030510 restraints weight = 130772.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.030758 restraints weight = 106102.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.030945 restraints weight = 94857.522| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 31648 Z= 0.147 Angle : 0.689 16.487 44409 Z= 0.373 Chirality : 0.046 0.448 4928 Planarity : 0.004 0.128 4342 Dihedral : 28.616 179.941 7236 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.48 % Favored : 94.41 % Rotamer: Outliers : 1.89 % Allowed : 21.06 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2735 helix: 0.58 (0.16), residues: 979 sheet: -1.29 (0.25), residues: 391 loop : -0.98 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 475 TYR 0.015 0.001 TYR G 308 PHE 0.019 0.001 PHE E 32 TRP 0.015 0.001 TRP E 60 HIS 0.006 0.001 HIS G 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (31645) covalent geometry : angle 0.68894 / 0.37 (44403) SS BOND : bond 0.00584 / 0.30 ( 3) SS BOND : angle 2.45574 / 1.39 ( 6) hydrogen bonds : bond 0.09917 / 6.70 ( 1181) hydrogen bonds : angle 4.95257 / 3.43 ( 2905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6580.71 seconds wall clock time: 114 minutes 28.32 seconds (6868.32 seconds total)