Starting phenix.real_space_refine on Thu Jun 26 00:11:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tb9_41146/06_2025/8tb9_41146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tb9_41146/06_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_41146/06_2025/8tb9_41146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tb9_41146/06_2025/8tb9_41146.map" model { file = "/net/cci-nas-00/data/ceres_data/8tb9_41146/06_2025/8tb9_41146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tb9_41146/06_2025/8tb9_41146.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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: 16.47, per 1000 atoms: 0.54 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: 6.68 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 12.64 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: 14.52 Time building geometry restraints manager: 8.11 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: 4.110 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: 1.250 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 74.440 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.910 ------------------------------------------------------------------------------- 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 : 25.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), 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 TRP 0.012 0.001 TRP O 235 HIS 0.011 0.001 HIS Y 260 PHE 0.018 0.001 PHE G 296 TYR 0.017 0.001 TYR A 27 ARG 0.012 0.000 ARG E 719 Details of bonding type rmsd hydrogen bonds : bond 0.31906 ( 1181) hydrogen bonds : angle 9.33102 ( 2905) SS BOND : bond 0.01215 ( 3) SS BOND : angle 3.11957 ( 6) covalent geometry : bond 0.00430 (31645) covalent geometry : angle 1.40203 (44403) *********************** 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 : 2.886 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: 0.4148 time to fit residues: 85.5108 Evaluate side-chains 121 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 260 optimal weight: 20.0000 chunk 234 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 520 ASN ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN E 618 HIS E 693 ASN G 157 ASN G 181 GLN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 382 GLN ** G 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 GLN I 113 HIS ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 93 GLN ** O 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN ** X 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.045967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.029001 restraints weight = 337881.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029516 restraints weight = 193118.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.029984 restraints weight = 137513.451| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 31648 Z= 0.276 Angle : 0.729 10.753 44409 Z= 0.405 Chirality : 0.043 0.238 4928 Planarity : 0.005 0.127 4342 Dihedral : 28.699 179.105 7243 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer: Outliers : 3.09 % Allowed : 17.40 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 2735 helix: 0.23 (0.15), residues: 982 sheet: -1.52 (0.23), residues: 395 loop : -1.01 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 255 HIS 0.007 0.001 HIS Y 260 PHE 0.023 0.002 PHE E 32 TYR 0.019 0.002 TYR S 37 ARG 0.016 0.001 ARG E 658 Details of bonding type rmsd hydrogen bonds : bond 0.10566 ( 1181) hydrogen bonds : angle 5.94021 ( 2905) SS BOND : bond 0.01586 ( 3) SS BOND : angle 2.97200 ( 6) covalent geometry : bond 0.00580 (31645) covalent geometry : angle 0.72868 (44403) *********************** 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 193 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 118 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7158 (tpt) REVERT: E 41 MET cc_start: 0.9484 (mpp) cc_final: 0.9107 (mpp) REVERT: E 111 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: E 681 ASP cc_start: 0.9265 (p0) cc_final: 0.8640 (t0) REVERT: G 213 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.8206 (m170) REVERT: O 36 MET cc_start: 0.8736 (mmp) cc_final: 0.6747 (tmm) REVERT: O 404 MET cc_start: 0.8575 (pmm) cc_final: 0.8254 (pmm) REVERT: W 106 ASP cc_start: 0.9290 (m-30) cc_final: 0.8999 (m-30) REVERT: W 120 MET cc_start: 0.8294 (mpp) cc_final: 0.7885 (mpp) REVERT: X 92 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.9095 (ttp80) outliers start: 75 outliers final: 30 residues processed: 180 average time/residue: 0.4213 time to fit residues: 123.6968 Evaluate side-chains 141 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 2.876 ------------------------------------------------------------------------------- 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 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 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 97 LEU Chi-restraints excluded: chain O residue 79 LEU 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 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 X residue 65 VAL Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 92 ARG Chi-restraints excluded: chain Y residue 242 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 268 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 277 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 502 ASN ** D 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 526 GLN ** 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** O 343 ASN O 383 ASN O 410 ASN R 89 ASN ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 HIS X 75 HIS Y 187 HIS Y 268 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.047348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.029972 restraints weight = 329204.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.030679 restraints weight = 181672.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.031178 restraints weight = 127923.420| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 31648 Z= 0.162 Angle : 0.634 8.898 44409 Z= 0.350 Chirality : 0.041 0.230 4928 Planarity : 0.005 0.126 4342 Dihedral : 28.555 178.595 7236 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 2.67 % Allowed : 18.02 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2735 helix: 0.56 (0.16), residues: 988 sheet: -1.47 (0.24), residues: 380 loop : -0.94 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 60 HIS 0.006 0.001 HIS Y 260 PHE 0.020 0.001 PHE E 32 TYR 0.014 0.001 TYR G 244 ARG 0.004 0.000 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.10389 ( 1181) hydrogen bonds : angle 5.26291 ( 2905) SS BOND : bond 0.00699 ( 3) SS BOND : angle 2.31702 ( 6) covalent geometry : bond 0.00349 (31645) covalent geometry : angle 0.63298 (44403) *********************** 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 188 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 123 time to evaluate : 7.891 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: 0.7450 (OUTLIER) cc_final: 0.7089 (tpt) REVERT: E 111 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: E 444 MET cc_start: 0.8519 (ppp) cc_final: 0.8295 (ppp) REVERT: E 681 ASP cc_start: 0.9336 (p0) cc_final: 0.8742 (t0) REVERT: G 213 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8421 (m170) REVERT: G 376 MET cc_start: 0.8312 (tpp) cc_final: 0.7955 (tpp) REVERT: I 67 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8113 (t80) REVERT: O 36 MET cc_start: 0.8572 (mmp) cc_final: 0.6653 (tmm) REVERT: O 37 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8759 (p) REVERT: S 81 ASN cc_start: 0.9199 (m-40) cc_final: 0.8868 (p0) REVERT: W 104 PHE cc_start: 0.9197 (m-80) cc_final: 0.8850 (m-80) REVERT: W 106 ASP cc_start: 0.9260 (m-30) cc_final: 0.8971 (m-30) outliers start: 65 outliers final: 32 residues processed: 178 average time/residue: 0.5100 time to fit residues: 153.3640 Evaluate side-chains 151 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 2.882 ------------------------------------------------------------------------------- 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 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 466 LYS 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 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 85 ASP 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 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain X residue 68 ASP 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 238 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 145 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 223 optimal weight: 2.9990 chunk 216 optimal weight: 40.0000 chunk 281 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 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 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 ASN ** E 526 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.046244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.029039 restraints weight = 336117.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.029743 restraints weight = 185857.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.030198 restraints weight = 131958.172| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 31648 Z= 0.216 Angle : 0.638 8.885 44409 Z= 0.355 Chirality : 0.041 0.301 4928 Planarity : 0.005 0.127 4342 Dihedral : 28.497 179.889 7236 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 3.09 % Allowed : 18.55 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2735 helix: 0.49 (0.16), residues: 983 sheet: -1.45 (0.24), residues: 390 loop : -0.94 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 60 HIS 0.005 0.001 HIS U 31 PHE 0.020 0.002 PHE E 32 TYR 0.016 0.002 TYR J 88 ARG 0.005 0.000 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.09692 ( 1181) hydrogen bonds : angle 5.20665 ( 2905) SS BOND : bond 0.01036 ( 3) SS BOND : angle 2.16560 ( 6) covalent geometry : bond 0.00467 (31645) covalent geometry : angle 0.63797 (44403) *********************** 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 194 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 119 time to evaluate : 2.786 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: 0.7609 (OUTLIER) cc_final: 0.7353 (tpt) REVERT: E 111 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: E 565 CYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6213 (t) REVERT: G 213 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8272 (m170) REVERT: G 376 MET cc_start: 0.8222 (tpp) cc_final: 0.7999 (tpp) REVERT: I 67 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8174 (t80) REVERT: O 36 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.6791 (tmm) REVERT: O 37 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8648 (p) REVERT: O 133 MET cc_start: 0.8783 (tmm) cc_final: 0.7759 (tmm) REVERT: S 81 ASN cc_start: 0.9165 (m-40) cc_final: 0.8846 (p0) REVERT: W 104 PHE cc_start: 0.9223 (m-80) cc_final: 0.8826 (m-80) REVERT: W 106 ASP cc_start: 0.9294 (m-30) cc_final: 0.9020 (m-30) REVERT: X 98 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7809 (m-80) outliers start: 75 outliers final: 42 residues processed: 181 average time/residue: 0.3883 time to fit residues: 116.4206 Evaluate side-chains 159 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 2.921 ------------------------------------------------------------------------------- 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 301 VAL 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 565 CYS Chi-restraints excluded: chain E residue 599 TRP Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 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 37 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 148 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 290 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 274 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** E 526 GLN ** 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** 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 = 0.3522 r_free = 0.3522 target = 0.045641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.028621 restraints weight = 335095.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.029256 restraints weight = 188868.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029701 restraints weight = 134758.912| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2844 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= 0.236 Angle : 0.661 10.662 44409 Z= 0.367 Chirality : 0.041 0.210 4928 Planarity : 0.005 0.127 4342 Dihedral : 28.602 179.065 7236 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.78 % Favored : 94.15 % Rotamer: Outliers : 3.87 % Allowed : 18.51 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2735 helix: 0.44 (0.16), residues: 984 sheet: -1.44 (0.24), residues: 399 loop : -0.96 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 60 HIS 0.016 0.001 HIS V 79 PHE 0.021 0.002 PHE E 32 TYR 0.014 0.002 TYR S 37 ARG 0.009 0.000 ARG G 169 Details of bonding type rmsd hydrogen bonds : bond 0.09668 ( 1181) hydrogen bonds : angle 5.20865 ( 2905) SS BOND : bond 0.01048 ( 3) SS BOND : angle 2.31946 ( 6) covalent geometry : bond 0.00509 (31645) covalent geometry : angle 0.66073 (44403) *********************** 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 206 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 112 time to evaluate : 2.594 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: 0.7831 (OUTLIER) cc_final: 0.7578 (tpt) REVERT: D 579 MET cc_start: 0.9517 (ttt) cc_final: 0.9274 (tpt) REVERT: E 110 MET cc_start: 0.8636 (ppp) cc_final: 0.8416 (tmm) REVERT: E 111 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: E 565 CYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6419 (t) REVERT: G 213 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8079 (m170) REVERT: G 376 MET cc_start: 0.8258 (tpp) cc_final: 0.7937 (tpp) REVERT: I 67 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8188 (t80) REVERT: O 140 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9257 (mp) REVERT: R 110 ASN cc_start: 0.9423 (OUTLIER) cc_final: 0.9129 (m110) REVERT: S 81 ASN cc_start: 0.9129 (m-40) cc_final: 0.8804 (p0) REVERT: W 104 PHE cc_start: 0.9281 (m-10) cc_final: 0.8910 (m-80) REVERT: W 106 ASP cc_start: 0.9300 (m-30) cc_final: 0.9034 (m-30) REVERT: X 98 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7449 (m-80) outliers start: 94 outliers final: 52 residues processed: 191 average time/residue: 0.4004 time to fit residues: 129.6554 Evaluate side-chains 170 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 110 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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 622 MET Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain E residue 45 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 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 179 THR 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 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 63 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 110 ASN 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 70 ILE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 187 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 143 optimal weight: 40.0000 chunk 54 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 221 optimal weight: 30.0000 chunk 186 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 526 GLN ** 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** ** W 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 187 HIS Y 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.046511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.029318 restraints weight = 327571.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030029 restraints weight = 182782.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.030491 restraints weight = 129043.965| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3073 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= 0.167 Angle : 0.629 13.896 44409 Z= 0.346 Chirality : 0.040 0.410 4928 Planarity : 0.004 0.128 4342 Dihedral : 28.502 179.460 7236 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.63 % Favored : 94.30 % Rotamer: Outliers : 2.84 % Allowed : 19.87 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2735 helix: 0.70 (0.17), residues: 980 sheet: -1.39 (0.25), residues: 390 loop : -0.93 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 49 HIS 0.006 0.001 HIS G 235 PHE 0.021 0.001 PHE E 32 TYR 0.018 0.001 TYR G 148 ARG 0.004 0.000 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.09596 ( 1181) hydrogen bonds : angle 4.91679 ( 2905) SS BOND : bond 0.00616 ( 3) SS BOND : angle 2.24487 ( 6) covalent geometry : bond 0.00366 (31645) covalent geometry : angle 0.62803 (44403) *********************** 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 191 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 122 time to evaluate : 3.419 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: 0.7891 (OUTLIER) cc_final: 0.7568 (tpt) REVERT: E 111 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: E 565 CYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6427 (t) REVERT: E 705 MET cc_start: 0.8635 (tpt) cc_final: 0.8415 (tpt) REVERT: G 213 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8342 (m170) REVERT: G 376 MET cc_start: 0.8276 (tpp) cc_final: 0.7947 (tpp) REVERT: I 67 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8157 (t80) REVERT: I 120 MET cc_start: 0.8324 (mpp) cc_final: 0.7934 (mpp) REVERT: O 36 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.6859 (tpp) REVERT: S 81 ASN cc_start: 0.9000 (m-40) cc_final: 0.8745 (p0) REVERT: W 104 PHE cc_start: 0.9209 (m-10) cc_final: 0.8818 (m-80) REVERT: W 106 ASP cc_start: 0.9306 (m-30) cc_final: 0.9041 (m-30) REVERT: X 98 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.7486 (m-80) outliers start: 69 outliers final: 47 residues processed: 179 average time/residue: 0.4154 time to fit residues: 123.0680 Evaluate side-chains 167 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET Chi-restraints excluded: chain O residue 52 ASP 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 54 LYS 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 70 ILE Chi-restraints excluded: chain V residue 87 THR 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 193 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 141 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 238 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 91 optimal weight: 0.0470 chunk 28 optimal weight: 8.9990 chunk 196 optimal weight: 30.0000 chunk 136 optimal weight: 0.3980 overall best weight: 3.2884 ------------------------------------------------------------------------------- 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 526 GLN ** 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 = 0.3539 r_free = 0.3539 target = 0.046219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.029153 restraints weight = 331563.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.029807 restraints weight = 185236.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.030276 restraints weight = 130859.185| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3207 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= 0.180 Angle : 0.636 13.693 44409 Z= 0.348 Chirality : 0.040 0.421 4928 Planarity : 0.004 0.128 4342 Dihedral : 28.427 179.738 7236 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 2.92 % Allowed : 20.32 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2735 helix: 0.67 (0.16), residues: 983 sheet: -1.30 (0.25), residues: 383 loop : -0.97 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 60 HIS 0.005 0.001 HIS D 659 PHE 0.023 0.001 PHE E 32 TYR 0.014 0.001 TYR G 148 ARG 0.004 0.000 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.09472 ( 1181) hydrogen bonds : angle 4.92540 ( 2905) SS BOND : bond 0.00678 ( 3) SS BOND : angle 2.14847 ( 6) covalent geometry : bond 0.00393 (31645) covalent geometry : angle 0.63532 (44403) *********************** 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 190 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 119 time to evaluate : 3.064 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: 0.7949 (OUTLIER) cc_final: 0.7495 (tpt) REVERT: E 41 MET cc_start: 0.9523 (mmm) cc_final: 0.9291 (mpp) REVERT: E 111 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: E 565 CYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6536 (t) REVERT: G 213 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8329 (m170) REVERT: G 376 MET cc_start: 0.8278 (tpp) cc_final: 0.7955 (tpp) REVERT: I 67 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8142 (t80) REVERT: O 36 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: O 140 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9250 (mp) REVERT: S 81 ASN cc_start: 0.8985 (m-40) cc_final: 0.8763 (p0) REVERT: W 104 PHE cc_start: 0.9223 (m-10) cc_final: 0.8817 (m-80) REVERT: W 106 ASP cc_start: 0.9305 (m-30) cc_final: 0.9041 (m-30) REVERT: X 98 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7514 (m-80) outliers start: 71 outliers final: 54 residues processed: 177 average time/residue: 0.3864 time to fit residues: 113.4534 Evaluate side-chains 180 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 118 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 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 599 TRP Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 213 HIS Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain G residue 258 HIS Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 298 ASP 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 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET 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 140 ILE Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 54 LYS 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 70 ILE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 68 ASP Chi-restraints excluded: chain X residue 98 TYR Chi-restraints excluded: chain Y residue 242 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 183 optimal weight: 0.9990 chunk 297 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 238 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 199 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 212 GLN ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** 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 406 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.045470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.028374 restraints weight = 335333.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.029055 restraints weight = 190318.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029504 restraints weight = 135559.954| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3466 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= 0.227 Angle : 0.667 13.971 44409 Z= 0.365 Chirality : 0.041 0.439 4928 Planarity : 0.005 0.129 4342 Dihedral : 28.517 179.128 7236 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 3.25 % Allowed : 20.44 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2735 helix: 0.50 (0.16), residues: 991 sheet: -1.27 (0.25), residues: 379 loop : -0.97 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 113 HIS 0.005 0.001 HIS G 235 PHE 0.024 0.001 PHE E 32 TYR 0.013 0.002 TYR S 37 ARG 0.007 0.000 ARG D 516 Details of bonding type rmsd hydrogen bonds : bond 0.09540 ( 1181) hydrogen bonds : angle 5.07382 ( 2905) SS BOND : bond 0.00930 ( 3) SS BOND : angle 2.15880 ( 6) covalent geometry : bond 0.00493 (31645) covalent geometry : angle 0.66643 (44403) *********************** 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 194 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 115 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7582 (tpt) REVERT: E 111 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: E 565 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6652 (t) REVERT: G 213 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8240 (m170) REVERT: G 376 MET cc_start: 0.8277 (tpp) cc_final: 0.7960 (tpp) REVERT: I 67 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8208 (t80) REVERT: O 36 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7863 (mmm) REVERT: O 140 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9252 (mp) REVERT: O 397 ASN cc_start: 0.7381 (OUTLIER) cc_final: 0.6615 (m-40) REVERT: S 68 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8398 (tp30) REVERT: S 81 ASN cc_start: 0.9041 (m-40) cc_final: 0.8795 (p0) REVERT: W 104 PHE cc_start: 0.9291 (m-10) cc_final: 0.8907 (m-80) REVERT: W 106 ASP cc_start: 0.9329 (m-30) cc_final: 0.9064 (m-30) REVERT: X 98 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7469 (m-80) outliers start: 79 outliers final: 55 residues processed: 182 average time/residue: 0.5613 time to fit residues: 169.0518 Evaluate side-chains 176 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 112 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LYS 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 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 465 THR 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 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 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 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET 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 140 ILE Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 382 TRP Chi-restraints excluded: chain O residue 397 ASN 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 45 VAL Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 70 ILE 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 70 ILE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 54 THR 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 170 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 34 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 302 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** 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 406 HIS ** 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 = 0.3512 r_free = 0.3512 target = 0.045420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.028624 restraints weight = 345043.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029473 restraints weight = 204348.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.029429 restraints weight = 130582.102| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 31648 Z= 0.226 Angle : 0.675 13.813 44409 Z= 0.369 Chirality : 0.041 0.439 4928 Planarity : 0.005 0.129 4342 Dihedral : 28.630 178.929 7236 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 3.13 % Allowed : 20.73 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2735 helix: 0.48 (0.16), residues: 984 sheet: -1.23 (0.25), residues: 392 loop : -0.96 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 218 HIS 0.008 0.001 HIS V 106 PHE 0.023 0.002 PHE E 32 TYR 0.014 0.002 TYR S 37 ARG 0.005 0.000 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.09549 ( 1181) hydrogen bonds : angle 5.06476 ( 2905) SS BOND : bond 0.00878 ( 3) SS BOND : angle 2.31500 ( 6) covalent geometry : bond 0.00488 (31645) covalent geometry : angle 0.67469 (44403) *********************** 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 189 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 113 time to evaluate : 2.913 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: D 118 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7447 (tpt) REVERT: E 111 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: E 565 CYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6782 (t) REVERT: E 705 MET cc_start: 0.8682 (tpt) cc_final: 0.8397 (mmm) REVERT: G 213 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8187 (m170) REVERT: G 376 MET cc_start: 0.8226 (tpp) cc_final: 0.7939 (tpp) REVERT: I 67 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8202 (t80) REVERT: O 36 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.6895 (tpp) REVERT: O 140 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9254 (mp) REVERT: O 397 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.6658 (m-40) REVERT: S 68 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8413 (tp30) REVERT: S 81 ASN cc_start: 0.8983 (m-40) cc_final: 0.8758 (p0) REVERT: W 104 PHE cc_start: 0.9306 (m-10) cc_final: 0.8896 (m-80) REVERT: W 106 ASP cc_start: 0.9353 (m-30) cc_final: 0.9082 (m-30) REVERT: W 120 MET cc_start: 0.8450 (mpp) cc_final: 0.8244 (mpp) REVERT: X 98 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7360 (m-80) outliers start: 76 outliers final: 55 residues processed: 177 average time/residue: 0.4097 time to fit residues: 120.3950 Evaluate side-chains 174 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 110 time to evaluate : 2.895 ------------------------------------------------------------------------------- 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 162 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 663 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 465 THR 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 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 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 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET 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 140 ILE Chi-restraints excluded: chain O residue 313 PHE Chi-restraints excluded: chain O residue 397 ASN 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 54 LYS Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 70 ILE 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 45 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 54 THR 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 170 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 15 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 266 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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** ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 ASN ** 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** Y 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.045853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.029200 restraints weight = 334744.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030022 restraints weight = 189324.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.030113 restraints weight = 120159.557| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3891 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= 0.184 Angle : 0.668 16.026 44409 Z= 0.359 Chirality : 0.041 0.460 4928 Planarity : 0.005 0.129 4342 Dihedral : 28.548 178.613 7236 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.22 % Favored : 93.67 % Rotamer: Outliers : 2.55 % Allowed : 21.27 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2735 helix: 0.63 (0.17), residues: 985 sheet: -1.24 (0.25), residues: 390 loop : -0.97 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP O 382 HIS 0.006 0.001 HIS D 659 PHE 0.023 0.001 PHE E 32 TYR 0.016 0.001 TYR S 34 ARG 0.005 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.09460 ( 1181) hydrogen bonds : angle 4.94281 ( 2905) SS BOND : bond 0.00654 ( 3) SS BOND : angle 2.25041 ( 6) covalent geometry : bond 0.00403 (31645) covalent geometry : angle 0.66748 (44403) ********************** 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 179 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 117 time to evaluate : 3.089 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: 0.8169 (OUTLIER) cc_final: 0.7764 (tpt) REVERT: E 111 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: E 565 CYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6861 (t) REVERT: E 705 MET cc_start: 0.8660 (tpt) cc_final: 0.8421 (mmm) REVERT: G 213 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8400 (m170) REVERT: G 376 MET cc_start: 0.8305 (tpp) cc_final: 0.7998 (tpp) REVERT: I 67 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8158 (t80) REVERT: O 36 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6842 (tpp) REVERT: O 140 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9231 (mp) REVERT: R 110 ASN cc_start: 0.9456 (OUTLIER) cc_final: 0.9114 (m110) REVERT: S 68 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8354 (tp30) REVERT: S 81 ASN cc_start: 0.8981 (m-40) cc_final: 0.8761 (p0) REVERT: W 104 PHE cc_start: 0.9254 (m-10) cc_final: 0.8818 (m-80) REVERT: W 106 ASP cc_start: 0.9343 (m-30) cc_final: 0.9134 (m-30) REVERT: W 120 MET cc_start: 0.8480 (mpp) cc_final: 0.8264 (mpp) REVERT: X 98 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7486 (m-80) outliers start: 62 outliers final: 50 residues processed: 168 average time/residue: 0.3975 time to fit residues: 111.7717 Evaluate side-chains 176 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 117 time to evaluate : 2.711 ------------------------------------------------------------------------------- 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 162 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 663 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 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 213 HIS Chi-restraints excluded: chain G residue 226 VAL 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 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 85 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain O residue 36 MET 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 140 ILE 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 54 LYS 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 70 ILE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain X residue 54 THR 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 170 ASN Chi-restraints excluded: chain Y residue 248 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 181 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 567 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** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 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** 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 = 0.045191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.028308 restraints weight = 346519.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.028816 restraints weight = 198782.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.029238 restraints weight = 139851.323| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4069 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= 0.222 Angle : 0.682 15.279 44409 Z= 0.368 Chirality : 0.041 0.453 4928 Planarity : 0.005 0.129 4342 Dihedral : 28.538 178.396 7236 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.22 % Favored : 93.67 % Rotamer: Outliers : 2.71 % Allowed : 21.14 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2735 helix: 0.58 (0.16), residues: 977 sheet: -1.11 (0.25), residues: 395 loop : -1.06 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 113 HIS 0.010 0.001 HIS E 711 PHE 0.023 0.002 PHE E 32 TYR 0.016 0.002 TYR S 34 ARG 0.005 0.000 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.09492 ( 1181) hydrogen bonds : angle 5.03644 ( 2905) SS BOND : bond 0.00853 ( 3) SS BOND : angle 2.20199 ( 6) covalent geometry : bond 0.00482 (31645) covalent geometry : angle 0.68113 (44403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13238.14 seconds wall clock time: 237 minutes 58.12 seconds (14278.12 seconds total)