Starting phenix.real_space_refine on Mon Aug 25 18:42:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tb9_41146/08_2025/8tb9_41146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tb9_41146/08_2025/8tb9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2025/8tb9_41146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2025/8tb9_41146.map" model { file = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2025/8tb9_41146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tb9_41146/08_2025/8tb9_41146.cif" } 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-2.0-5787/lib/python3.9/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: 6.95, per 1000 atoms: 0.23 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: 2.66 Conformation dependent library (CDL) restraints added in 972.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 5.00 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: 7.68 Time building geometry restraints manager: 3.48 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=" C2 SAH E 801 " pdb=" N3 SAH E 801 " ideal model delta sigma weight residual 1.322 1.382 -0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" C8 SAH E 801 " pdb=" N7 SAH E 801 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C2 SAH E 801 " pdb=" N1 SAH E 801 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C6 SAH E 801 " pdb=" N1 SAH E 801 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.01e+00 bond pdb=" CB PRO E 327 " pdb=" CG PRO E 327 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.72e+00 ... (remaining 31640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 43654 3.89 - 7.78: 163 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 - 0.124: 4593 0.124 - 0.247: 22 0.247 - 0.371: 91 0.371 - 0.494: 204 0.494 - 0.618: 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 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.54e+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 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.00e+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 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.81e+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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 32.960 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.004 0.096 31648 Z= 0.205 Angle : 1.402 19.458 44409 Z= 0.560 Chirality : 0.107 0.618 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 aren 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 covalent geometry : bond 0.00430 (31645) covalent geometry : angle 1.40203 (44403) SS BOND : bond 0.01215 ( 3) SS BOND : angle 3.11957 ( 6) hydrogen bonds : bond 0.31906 ( 1181) hydrogen bonds : angle 9.33102 ( 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 : 1.049 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: 0.2076 time to fit residues: 42.6600 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 : 1.131 ------------------------------------------------------------------------------- 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: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0570 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 221 GLN D 517 ASN ** D 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 382 GLN ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 HIS ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 ASN O 383 ASN O 385 ASN 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** W 39 HIS X 27 GLN X 75 HIS Y 187 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.046676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.029592 restraints weight = 333867.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.030152 restraints weight = 189701.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.030634 restraints weight = 133571.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.030891 restraints weight = 108451.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.031084 restraints weight = 96724.425| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 31648 Z= 0.222 Angle : 0.696 10.077 44409 Z= 0.387 Chirality : 0.043 0.239 4928 Planarity : 0.005 0.126 4342 Dihedral : 28.569 179.105 7243 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 2.80 % Allowed : 17.28 % Favored : 79.93 % 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 aren not related in a simple way. whole: -0.91 (0.15), residues: 2735 helix: 0.34 (0.15), residues: 983 sheet: -1.42 (0.24), residues: 376 loop : -1.01 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 129 TYR 0.016 0.002 TYR S 37 PHE 0.024 0.002 PHE W 104 TRP 0.011 0.002 TRP E 60 HIS 0.007 0.001 HIS Y 260 Details of bonding type rmsd covalent geometry : bond 0.00470 (31645) covalent geometry : angle 0.69572 (44403) SS BOND : bond 0.01309 ( 3) SS BOND : angle 2.69940 ( 6) hydrogen bonds : bond 0.10836 ( 1181) hydrogen bonds : angle 5.86057 ( 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 192 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 124 time to evaluate : 1.074 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 118 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7266 (tpt) REVERT: E 41 MET cc_start: 0.9493 (mpp) cc_final: 0.9170 (mpp) REVERT: E 111 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: E 681 ASP cc_start: 0.9226 (p0) cc_final: 0.8713 (t0) REVERT: E 705 MET cc_start: 0.8575 (tpt) cc_final: 0.8161 (mmm) REVERT: E 706 MET cc_start: 0.9211 (tpp) cc_final: 0.8994 (tpp) REVERT: G 213 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8186 (m90) REVERT: O 36 MET cc_start: 0.8641 (mmp) cc_final: 0.6598 (tmm) REVERT: O 383 ASN cc_start: 0.6676 (OUTLIER) cc_final: 0.6291 (p0) REVERT: O 404 MET cc_start: 0.8543 (pmm) cc_final: 0.8211 (pmm) REVERT: W 104 PHE cc_start: 0.9199 (m-80) cc_final: 0.8948 (m-80) REVERT: W 106 ASP cc_start: 0.9227 (m-30) cc_final: 0.8946 (m-30) REVERT: X 92 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.9100 (ttp80) REVERT: Y 288 MET cc_start: 0.8717 (ttt) cc_final: 0.8316 (tmm) outliers start: 68 outliers final: 29 residues processed: 179 average time/residue: 0.2028 time to fit residues: 59.3073 Evaluate side-chains 149 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 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 66 VAL Chi-restraints excluded: chain V residue 70 ILE 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 242 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 290 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 298 optimal weight: 0.3980 chunk 4 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 overall best weight: 5.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 HIS ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 GLN J 93 GLN ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 343 ASN O 383 ASN O 410 ASN R 89 ASN ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Y 268 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.045995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.028795 restraints weight = 337672.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.029507 restraints weight = 190987.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.029935 restraints weight = 135551.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.030252 restraints weight = 111845.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.030374 restraints weight = 98895.688| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 31648 Z= 0.242 Angle : 0.669 9.339 44409 Z= 0.372 Chirality : 0.041 0.225 4928 Planarity : 0.005 0.126 4342 Dihedral : 28.592 179.232 7236 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 3.09 % Allowed : 18.35 % Favored : 78.57 % 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 aren not related in a simple way. whole: -0.95 (0.15), residues: 2735 helix: 0.34 (0.16), residues: 987 sheet: -1.62 (0.23), residues: 395 loop : -0.98 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 29 TYR 0.014 0.002 TYR V 37 PHE 0.021 0.002 PHE E 32 TRP 0.011 0.002 TRP E 60 HIS 0.025 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00522 (31645) covalent geometry : angle 0.66854 (44403) SS BOND : bond 0.01166 ( 3) SS BOND : angle 2.51624 ( 6) hydrogen bonds : bond 0.10227 ( 1181) hydrogen bonds : angle 5.56049 ( 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 190 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 115 time to evaluate : 1.081 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 118 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7266 (tpt) REVERT: E 111 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: E 444 MET cc_start: 0.8559 (ppp) cc_final: 0.8332 (ppp) REVERT: E 706 MET cc_start: 0.9234 (tpp) cc_final: 0.8873 (tpp) REVERT: G 213 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8010 (m170) REVERT: I 67 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8165 (t80) REVERT: O 36 MET cc_start: 0.8641 (mmp) cc_final: 0.6780 (tmm) REVERT: O 37 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8750 (p) REVERT: O 404 MET cc_start: 0.8519 (pmm) cc_final: 0.8309 (pmm) REVERT: S 81 ASN cc_start: 0.9266 (m-40) cc_final: 0.8865 (p0) REVERT: W 104 PHE cc_start: 0.9222 (m-80) cc_final: 0.8897 (m-80) REVERT: W 106 ASP cc_start: 0.9253 (m-30) cc_final: 0.8942 (m-30) REVERT: X 92 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.9136 (ttp80) outliers start: 75 outliers final: 42 residues processed: 178 average time/residue: 0.2033 time to fit residues: 59.1278 Evaluate side-chains 159 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 662 SER 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 509 ARG 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 267 SER 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 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 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 ILE 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 65 VAL Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 92 ARG Chi-restraints excluded: chain Y residue 194 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 123 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** 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 = 0.3537 r_free = 0.3537 target = 0.046215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.029099 restraints weight = 334700.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.029709 restraints weight = 188333.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.030143 restraints weight = 133087.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.030463 restraints weight = 109732.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.030623 restraints weight = 97759.761| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 31648 Z= 0.210 Angle : 0.644 9.249 44409 Z= 0.358 Chirality : 0.041 0.336 4928 Planarity : 0.005 0.126 4342 Dihedral : 28.598 179.265 7236 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.21 % Allowed : 18.47 % Favored : 78.32 % 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 aren not related in a simple way. whole: -0.85 (0.16), residues: 2735 helix: 0.43 (0.16), residues: 988 sheet: -1.46 (0.24), residues: 382 loop : -0.97 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 475 TYR 0.017 0.001 TYR X 72 PHE 0.020 0.002 PHE E 32 TRP 0.013 0.001 TRP E 60 HIS 0.006 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00453 (31645) covalent geometry : angle 0.64337 (44403) SS BOND : bond 0.01057 ( 3) SS BOND : angle 2.37666 ( 6) hydrogen bonds : bond 0.09694 ( 1181) hydrogen bonds : angle 5.26380 ( 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 200 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 122 time to evaluate : 1.041 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 118 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7394 (tpt) REVERT: E 111 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: E 565 CYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6250 (t) REVERT: E 706 MET cc_start: 0.9209 (tpp) cc_final: 0.8886 (tpp) REVERT: G 376 MET cc_start: 0.8276 (tpp) cc_final: 0.7900 (tpp) REVERT: I 67 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8164 (t80) REVERT: O 36 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.6765 (tmm) REVERT: O 37 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8514 (p) REVERT: S 68 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8249 (tp30) REVERT: S 81 ASN cc_start: 0.9166 (m-40) cc_final: 0.8821 (p0) REVERT: W 82 LEU cc_start: 0.7811 (mt) cc_final: 0.7590 (pt) REVERT: W 104 PHE cc_start: 0.9241 (m-80) cc_final: 0.8827 (m-80) REVERT: W 106 ASP cc_start: 0.9281 (m-30) cc_final: 0.9013 (m-30) REVERT: X 98 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7728 (m-80) outliers start: 78 outliers final: 44 residues processed: 185 average time/residue: 0.1983 time to fit residues: 60.2098 Evaluate side-chains 163 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 607 ASN Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 111 TYR 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 565 CYS Chi-restraints excluded: chain E residue 567 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 267 SER 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 I residue 90 MET Chi-restraints excluded: chain J residue 34 ILE 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 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 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 54 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 66 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 241 optimal weight: 1.9990 chunk 23 optimal weight: 50.0000 chunk 40 optimal weight: 50.0000 chunk 38 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** 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** S 106 HIS ** 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 = 0.3544 r_free = 0.3544 target = 0.046494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.029341 restraints weight = 328655.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.029986 restraints weight = 184334.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.030414 restraints weight = 130137.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.030736 restraints weight = 107429.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.030878 restraints weight = 95227.734| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 31648 Z= 0.183 Angle : 0.627 9.233 44409 Z= 0.348 Chirality : 0.040 0.212 4928 Planarity : 0.005 0.127 4342 Dihedral : 28.488 179.131 7236 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.37 % Allowed : 18.68 % Favored : 77.95 % 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 aren not related in a simple way. whole: -0.72 (0.16), residues: 2735 helix: 0.57 (0.16), residues: 986 sheet: -1.45 (0.24), residues: 399 loop : -0.89 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 169 TYR 0.018 0.001 TYR G 148 PHE 0.019 0.001 PHE E 32 TRP 0.013 0.001 TRP E 60 HIS 0.006 0.001 HIS R 82 Details of bonding type rmsd covalent geometry : bond 0.00400 (31645) covalent geometry : angle 0.62695 (44403) SS BOND : bond 0.00768 ( 3) SS BOND : angle 2.28211 ( 6) hydrogen bonds : bond 0.09617 ( 1181) hydrogen bonds : angle 5.04960 ( 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 207 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 125 time to evaluate : 1.051 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: D 118 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7448 (tpt) REVERT: E 111 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: E 565 CYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6347 (t) REVERT: E 706 MET cc_start: 0.9175 (tpp) cc_final: 0.8932 (tpp) REVERT: G 213 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8137 (m170) REVERT: G 376 MET cc_start: 0.8213 (tpp) cc_final: 0.7975 (tpp) REVERT: I 67 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8157 (t80) REVERT: O 133 MET cc_start: 0.8712 (tmm) cc_final: 0.7714 (tmm) REVERT: S 81 ASN cc_start: 0.9062 (m-40) cc_final: 0.8791 (p0) REVERT: W 104 PHE cc_start: 0.9225 (m-10) cc_final: 0.8871 (m-80) REVERT: W 106 ASP cc_start: 0.9268 (m-30) cc_final: 0.8998 (m-30) REVERT: X 98 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7567 (m-80) outliers start: 82 outliers final: 50 residues processed: 192 average time/residue: 0.1976 time to fit residues: 62.5915 Evaluate side-chains 172 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 79 VAL 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 199 VAL Chi-restraints excluded: chain D residue 296 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 109 ILE 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 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 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 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 30 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 93 LEU Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 66 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 25 optimal weight: 7.9990 chunk 146 optimal weight: 30.0000 chunk 83 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 201 optimal weight: 20.0000 chunk 268 optimal weight: 8.9990 chunk 262 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 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** ** W 68 GLN ** 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 = 0.3531 r_free = 0.3531 target = 0.046053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.029014 restraints weight = 332191.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029590 restraints weight = 187847.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.030048 restraints weight = 132014.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.030288 restraints weight = 107350.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.030365 restraints weight = 95967.616| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 31648 Z= 0.210 Angle : 0.640 12.553 44409 Z= 0.354 Chirality : 0.040 0.352 4928 Planarity : 0.005 0.128 4342 Dihedral : 28.465 179.833 7236 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 3.37 % Allowed : 19.29 % Favored : 77.33 % 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 aren not related in a simple way. whole: -0.76 (0.16), residues: 2735 helix: 0.55 (0.16), residues: 983 sheet: -1.47 (0.24), residues: 403 loop : -0.93 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG V 76 TYR 0.013 0.001 TYR S 37 PHE 0.019 0.001 PHE E 32 TRP 0.012 0.001 TRP E 60 HIS 0.018 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00457 (31645) covalent geometry : angle 0.63939 (44403) SS BOND : bond 0.00893 ( 3) SS BOND : angle 2.30872 ( 6) hydrogen bonds : bond 0.09487 ( 1181) hydrogen bonds : angle 5.07919 ( 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 205 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 123 time to evaluate : 1.039 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: D 118 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7470 (tpt) REVERT: E 41 MET cc_start: 0.9386 (mmt) cc_final: 0.9116 (mpp) REVERT: E 111 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: E 565 CYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6455 (t) REVERT: E 706 MET cc_start: 0.9180 (tpp) cc_final: 0.8896 (tpp) REVERT: G 213 HIS cc_start: 0.9180 (OUTLIER) cc_final: 0.8607 (m170) REVERT: G 376 MET cc_start: 0.8199 (tpp) cc_final: 0.7962 (tpp) REVERT: I 67 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8167 (t80) REVERT: I 120 MET cc_start: 0.8291 (mpp) cc_final: 0.7884 (mpp) REVERT: O 36 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.6580 (tmm) REVERT: R 110 ASN cc_start: 0.9410 (OUTLIER) cc_final: 0.9129 (m110) REVERT: S 81 ASN cc_start: 0.9045 (m-40) cc_final: 0.8772 (p0) REVERT: W 104 PHE cc_start: 0.9264 (m-10) cc_final: 0.8906 (m-80) REVERT: W 106 ASP cc_start: 0.9277 (m-30) cc_final: 0.9017 (m-30) REVERT: X 98 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.7405 (m-80) outliers start: 82 outliers final: 58 residues processed: 188 average time/residue: 0.1889 time to fit residues: 58.9168 Evaluate side-chains 182 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 116 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 79 VAL 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 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 662 SER 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 509 ARG Chi-restraints excluded: chain E residue 565 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 267 SER 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 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 30 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 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 242 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 24 optimal weight: 50.0000 chunk 72 optimal weight: 3.9990 chunk 196 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** 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** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Y 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.046427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.029411 restraints weight = 329172.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.029981 restraints weight = 185770.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030454 restraints weight = 130588.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.030707 restraints weight = 105781.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.030896 restraints weight = 94476.981| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 31648 Z= 0.174 Angle : 0.634 13.999 44409 Z= 0.347 Chirality : 0.040 0.421 4928 Planarity : 0.004 0.128 4342 Dihedral : 28.422 179.833 7236 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 3.00 % Allowed : 19.74 % Favored : 77.25 % 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 aren not related in a simple way. whole: -0.67 (0.16), residues: 2735 helix: 0.67 (0.16), residues: 979 sheet: -1.31 (0.25), residues: 389 loop : -0.95 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 76 TYR 0.022 0.001 TYR G 148 PHE 0.020 0.001 PHE E 32 TRP 0.013 0.001 TRP E 60 HIS 0.006 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00380 (31645) covalent geometry : angle 0.63371 (44403) SS BOND : bond 0.00653 ( 3) SS BOND : angle 2.28293 ( 6) hydrogen bonds : bond 0.09545 ( 1181) hydrogen bonds : angle 4.89152 ( 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 193 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 120 time to evaluate : 1.027 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: 0.7922 (OUTLIER) cc_final: 0.7666 (tpt) REVERT: E 111 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: E 565 CYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6582 (t) REVERT: E 706 MET cc_start: 0.9146 (tpp) cc_final: 0.8897 (tpp) REVERT: G 376 MET cc_start: 0.8285 (tpp) cc_final: 0.8056 (tpp) REVERT: I 67 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8173 (t80) REVERT: O 36 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.6623 (tmm) REVERT: R 110 ASN cc_start: 0.9430 (OUTLIER) cc_final: 0.9167 (m110) REVERT: W 104 PHE cc_start: 0.9239 (m-10) cc_final: 0.8841 (m-80) REVERT: W 106 ASP cc_start: 0.9268 (m-30) cc_final: 0.9037 (m-30) REVERT: X 98 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.7429 (m-80) outliers start: 73 outliers final: 48 residues processed: 178 average time/residue: 0.1909 time to fit residues: 56.8716 Evaluate side-chains 170 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 199 VAL Chi-restraints excluded: chain D residue 296 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 109 ILE 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 565 CYS Chi-restraints excluded: chain E residue 567 CYS Chi-restraints excluded: chain E residue 588 ASP 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 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 267 SER 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 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 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 65 LEU 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 66 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 112 optimal weight: 0.6980 chunk 208 optimal weight: 20.0000 chunk 264 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 58 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 251 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 634 HIS ** E 297 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** ** W 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Y 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.047859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.030533 restraints weight = 324398.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.031322 restraints weight = 179727.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.031834 restraints weight = 125789.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.032098 restraints weight = 101823.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.032303 restraints weight = 90801.623| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3476 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= 0.138 Angle : 0.627 15.321 44409 Z= 0.340 Chirality : 0.040 0.416 4928 Planarity : 0.004 0.128 4342 Dihedral : 28.156 179.471 7236 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % 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 aren not related in a simple way. whole: -0.53 (0.16), residues: 2735 helix: 0.81 (0.17), residues: 983 sheet: -1.21 (0.25), residues: 384 loop : -0.90 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.017 0.001 TYR G 148 PHE 0.020 0.001 PHE E 32 TRP 0.016 0.001 TRP E 60 HIS 0.005 0.001 HIS Y 260 Details of bonding type rmsd covalent geometry : bond 0.00303 (31645) covalent geometry : angle 0.62693 (44403) SS BOND : bond 0.00301 ( 3) SS BOND : angle 2.24374 ( 6) hydrogen bonds : bond 0.10399 ( 1181) hydrogen bonds : angle 4.57049 ( 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 187 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 1.082 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: 0.7813 (OUTLIER) cc_final: 0.7296 (tpt) REVERT: E 111 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: E 565 CYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6434 (t) REVERT: E 681 ASP cc_start: 0.9259 (p0) cc_final: 0.8726 (t0) REVERT: E 705 MET cc_start: 0.8720 (tpt) cc_final: 0.8500 (tpt) REVERT: G 376 MET cc_start: 0.8292 (tpp) cc_final: 0.8058 (tpp) REVERT: I 67 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.7998 (t80) REVERT: I 97 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8426 (mm-30) REVERT: O 36 MET cc_start: 0.8295 (mmp) cc_final: 0.6600 (tmm) REVERT: O 133 MET cc_start: 0.9123 (ppp) cc_final: 0.8882 (ppp) REVERT: R 110 ASN cc_start: 0.9447 (OUTLIER) cc_final: 0.9190 (m110) REVERT: S 68 GLU cc_start: 0.8772 (mm-30) cc_final: 0.7967 (tp30) REVERT: W 104 PHE cc_start: 0.9220 (m-10) cc_final: 0.8857 (m-80) REVERT: W 106 ASP cc_start: 0.9204 (m-30) cc_final: 0.8920 (m-30) REVERT: W 120 MET cc_start: 0.8498 (mpp) cc_final: 0.8275 (mpp) outliers start: 46 outliers final: 36 residues processed: 179 average time/residue: 0.2042 time to fit residues: 59.8200 Evaluate side-chains 162 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 509 ARG Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 567 CYS Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 313 ARG 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 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 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 U residue 78 ILE Chi-restraints excluded: chain V residue 49 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 Y residue 194 THR 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: 2.9990 chunk 272 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 232 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 290 optimal weight: 0.2980 chunk 305 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 415 GLN O 64 HIS U 104 GLN ** V 79 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.046371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.029274 restraints weight = 328397.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.029993 restraints weight = 184004.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.030470 restraints weight = 130297.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.030722 restraints weight = 106018.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.030901 restraints weight = 94781.653| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 31648 Z= 0.194 Angle : 0.646 13.985 44409 Z= 0.350 Chirality : 0.040 0.435 4928 Planarity : 0.004 0.129 4342 Dihedral : 28.151 179.981 7236 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 2.26 % Allowed : 21.35 % Favored : 76.39 % 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 aren not related in a simple way. whole: -0.54 (0.16), residues: 2735 helix: 0.81 (0.17), residues: 980 sheet: -1.11 (0.26), residues: 377 loop : -0.96 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 113 TYR 0.017 0.001 TYR G 148 PHE 0.019 0.001 PHE E 32 TRP 0.012 0.001 TRP E 113 HIS 0.008 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00426 (31645) covalent geometry : angle 0.64545 (44403) SS BOND : bond 0.00744 ( 3) SS BOND : angle 1.99341 ( 6) hydrogen bonds : bond 0.09375 ( 1181) hydrogen bonds : angle 4.77545 ( 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 171 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 1.088 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: 0.8131 (OUTLIER) cc_final: 0.7680 (tpt) REVERT: D 144 MET cc_start: 0.7871 (mmt) cc_final: 0.7445 (mpp) REVERT: E 111 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: E 565 CYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6679 (t) REVERT: G 376 MET cc_start: 0.8323 (tpp) cc_final: 0.7991 (tpp) REVERT: G 415 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8744 (mm-40) REVERT: I 67 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8153 (t80) REVERT: O 36 MET cc_start: 0.8366 (mmp) cc_final: 0.6637 (tmm) REVERT: R 110 ASN cc_start: 0.9419 (OUTLIER) cc_final: 0.9148 (m110) REVERT: W 104 PHE cc_start: 0.9311 (m-10) cc_final: 0.8891 (m-80) REVERT: W 106 ASP cc_start: 0.9272 (m-30) cc_final: 0.9006 (m-30) outliers start: 55 outliers final: 43 residues processed: 162 average time/residue: 0.1941 time to fit residues: 52.4164 Evaluate side-chains 161 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 667 ASN Chi-restraints excluded: chain E residue 109 ILE 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 565 CYS Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 258 HIS 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 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 52 ASP 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 30 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 U residue 78 ILE Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 70 ILE 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 81 VAL Chi-restraints excluded: chain Y residue 170 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 59 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 260 optimal weight: 20.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 GLN ** 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 = 0.3510 r_free = 0.3510 target = 0.045148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.028200 restraints weight = 341886.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.028769 restraints weight = 194922.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.029219 restraints weight = 138551.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.029443 restraints weight = 113614.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.029511 restraints weight = 102303.648| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 31648 Z= 0.256 Angle : 0.698 14.359 44409 Z= 0.381 Chirality : 0.042 0.451 4928 Planarity : 0.005 0.128 4342 Dihedral : 28.411 178.690 7236 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.44 % Favored : 93.46 % Rotamer: Outliers : 2.22 % Allowed : 21.43 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.79 (0.16), residues: 2735 helix: 0.47 (0.16), residues: 981 sheet: -1.17 (0.25), residues: 381 loop : -1.01 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 367 TYR 0.018 0.002 TYR G 148 PHE 0.032 0.002 PHE G 368 TRP 0.020 0.002 TRP E 113 HIS 0.014 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00556 (31645) covalent geometry : angle 0.69786 (44403) SS BOND : bond 0.01093 ( 3) SS BOND : angle 2.20507 ( 6) hydrogen bonds : bond 0.09682 ( 1181) hydrogen bonds : angle 5.12593 ( 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 169 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 115 time to evaluate : 1.047 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: D 118 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7952 (tpt) REVERT: E 111 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: E 315 ASN cc_start: -0.2015 (OUTLIER) cc_final: -0.2730 (t0) REVERT: E 565 CYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6759 (t) REVERT: G 376 MET cc_start: 0.8246 (tpp) cc_final: 0.7914 (tpp) REVERT: I 67 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8241 (t80) REVERT: O 36 MET cc_start: 0.8406 (mmp) cc_final: 0.6656 (tmm) REVERT: O 133 MET cc_start: 0.9229 (ppp) cc_final: 0.9026 (ppp) REVERT: R 110 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9105 (m110) REVERT: S 68 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8420 (tp30) REVERT: W 104 PHE cc_start: 0.9296 (m-10) cc_final: 0.8954 (m-80) REVERT: W 106 ASP cc_start: 0.9333 (m-30) cc_final: 0.9084 (m-30) outliers start: 54 outliers final: 41 residues processed: 160 average time/residue: 0.1915 time to fit residues: 51.1248 Evaluate side-chains 160 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 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 315 ASN Chi-restraints excluded: chain E residue 465 THR 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 258 HIS 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 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 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 R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 30 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 U residue 65 LEU Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain W residue 90 MET Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 170 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 300 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 281 optimal weight: 0.7980 chunk 143 optimal weight: 40.0000 chunk 134 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 HIS ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 ASN G 191 ASN G 213 HIS G 415 GLN ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.047246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.029983 restraints weight = 329262.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.030631 restraints weight = 183901.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.031133 restraints weight = 129067.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.031371 restraints weight = 104616.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.031544 restraints weight = 93717.103| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3880 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= 0.145 Angle : 0.652 15.944 44409 Z= 0.350 Chirality : 0.041 0.468 4928 Planarity : 0.004 0.128 4342 Dihedral : 28.264 179.110 7236 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 2.06 % Allowed : 21.84 % Favored : 76.10 % 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 aren not related in a simple way. whole: -0.51 (0.16), residues: 2735 helix: 0.78 (0.17), residues: 975 sheet: -0.97 (0.26), residues: 382 loop : -0.92 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 414 TYR 0.021 0.001 TYR G 148 PHE 0.019 0.001 PHE E 32 TRP 0.043 0.002 TRP O 382 HIS 0.006 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00319 (31645) covalent geometry : angle 0.65124 (44403) SS BOND : bond 0.00309 ( 3) SS BOND : angle 2.26061 ( 6) hydrogen bonds : bond 0.10181 ( 1181) hydrogen bonds : angle 4.67621 ( 2905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7486.41 seconds wall clock time: 130 minutes 5.83 seconds (7805.83 seconds total)