Starting phenix.real_space_refine on Sun Aug 24 18:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gw1_34302/08_2025/8gw1_34302_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gw1_34302/08_2025/8gw1_34302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gw1_34302/08_2025/8gw1_34302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gw1_34302/08_2025/8gw1_34302.map" model { file = "/net/cci-nas-00/data/ceres_data/8gw1_34302/08_2025/8gw1_34302_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gw1_34302/08_2025/8gw1_34302_neut.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 8 6.06 5 P 52 5.49 5 S 157 5.16 5 C 13678 2.51 5 N 3676 2.21 5 O 4270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21843 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7473 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 897} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "E" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'RNA': 1, 'peptide': 113} Modifications used: {'rna2p_pyr': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106, None: 1} Not linked: pdbres=" U G 0 " pdbres="ASN G 1 " Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 75.304 55.569 122.379 1.00 60.24 S ATOM 2487 SG CYS A 306 75.519 56.910 125.944 1.00 48.09 S ATOM 2519 SG CYS A 310 76.726 53.358 125.081 1.00 48.46 S ATOM 3927 SG CYS A 487 77.876 69.754 106.752 1.00 65.54 S ATOM 5180 SG CYS A 645 77.116 71.762 109.976 1.00 84.84 S ATOM 5186 SG CYS A 646 75.464 68.324 109.350 1.00 90.45 S ATOM 12030 SG CYS E 16 103.395 64.328 51.033 1.00189.89 S ATOM 12045 SG CYS E 19 104.166 60.960 49.289 1.00164.10 S ATOM 11948 SG CYS E 5 115.073 66.319 52.513 1.00156.12 S ATOM 11969 SG CYS E 8 116.595 68.752 50.276 1.00161.33 S ATOM 12107 SG CYS E 26 115.001 70.188 53.045 1.00149.12 S ATOM 12124 SG CYS E 29 112.834 68.396 49.974 1.00160.86 S ATOM 12289 SG CYS E 50 91.629 75.465 62.983 1.00150.56 S ATOM 12319 SG CYS E 55 88.830 74.112 60.779 1.00163.95 S ATOM 12452 SG CYS E 72 90.691 77.367 59.885 1.00156.12 S ATOM 16538 SG CYS F 16 60.494 74.857 67.000 1.00158.14 S ATOM 16553 SG CYS F 19 58.246 71.989 65.639 1.00170.85 S ATOM 16456 SG CYS F 5 69.641 70.707 59.223 1.00166.66 S ATOM 16477 SG CYS F 8 69.616 72.739 56.129 1.00157.20 S ATOM 16615 SG CYS F 26 70.876 74.352 59.097 1.00130.55 S ATOM 16632 SG CYS F 29 67.049 73.701 58.844 1.00154.89 S ATOM 16797 SG CYS F 50 66.543 87.762 81.021 1.00143.10 S ATOM 16827 SG CYS F 55 62.982 88.663 81.857 1.00183.79 S ATOM 16960 SG CYS F 72 64.938 90.764 79.343 1.00174.44 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.74 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.26 residue: pdb=" N AMET F 474 " occ=0.63 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.37 Time building chain proxies: 5.32, per 1000 atoms: 0.24 Number of scatterers: 21843 At special positions: 0 Unit cell: (153.34, 136.94, 185.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Mn 2 24.99 S 157 16.00 P 52 15.00 O 4270 8.00 N 3676 7.00 C 13678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 28 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 30 sheets defined 41.5% alpha, 14.4% beta 20 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 4.008A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.779A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.572A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.665A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.737A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.751A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.901A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.993A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.152A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.588A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.618A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.906A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.916A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.692A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.839A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.512A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.584A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.108A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 791 removed outlier: 4.005A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.081A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.960A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 4.447A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.987A pdb=" N THR A 926 " --> pdb=" O ALA A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.625A pdb=" N GLU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 95 removed outlier: 3.581A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.586A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.626A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.917A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.528A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 4.222A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.702A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 80 removed outlier: 4.149A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.580A pdb=" N ALA D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.537A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.711A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.723A pdb=" N LEU D 180 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 72 through 76 removed outlier: 3.946A pdb=" N LYS E 76 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.996A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 removed outlier: 3.611A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 262 through 267 removed outlier: 3.658A pdb=" N ALA E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.796A pdb=" N LEU E 295 " --> pdb=" O PHE E 291 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.616A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 removed outlier: 3.753A pdb=" N TYR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 380 through 391 removed outlier: 3.693A pdb=" N VAL E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN E 388 " --> pdb=" O LEU E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 removed outlier: 3.671A pdb=" N PHE E 422 " --> pdb=" O PRO E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 429 Processing helix chain 'E' and resid 445 through 454 removed outlier: 4.332A pdb=" N THR E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 501 removed outlier: 3.891A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 509 removed outlier: 3.898A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 509 " --> pdb=" O TRP E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 526 removed outlier: 3.764A pdb=" N ASN E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.976A pdb=" N ASN E 557 " --> pdb=" O ALA E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 116 through 126 removed outlier: 4.086A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 3.539A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 268 removed outlier: 3.834A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 275 removed outlier: 3.883A pdb=" N VAL F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.878A pdb=" N ALA F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.808A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 329 Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.599A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 422 removed outlier: 3.658A pdb=" N PHE F 422 " --> pdb=" O PRO F 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 419 through 422' Processing helix chain 'F' and resid 423 through 429 removed outlier: 3.857A pdb=" N LEU F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET F 429 " --> pdb=" O VAL F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 454 removed outlier: 3.602A pdb=" N ASP F 450 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 503 removed outlier: 3.648A pdb=" N ARG F 497 " --> pdb=" O ILE F 493 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU F 498 " --> pdb=" O GLY F 494 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG F 502 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN F 503 " --> pdb=" O PHE F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 509 removed outlier: 4.211A pdb=" N LYS F 508 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.869A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 536 No H-bonds generated for 'chain 'F' and resid 534 through 536' Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.332A pdb=" N CYS A 54 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 70 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 114 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.613A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 669 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 189 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757 removed outlier: 3.946A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.910A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.520A pdb=" N LEU D 184 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 149 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.520A pdb=" N LEU D 184 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.515A pdb=" N GLY E 3 " --> pdb=" O THR E 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.683A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 85 removed outlier: 4.069A pdb=" N ALA E 85 " --> pdb=" O GLN E 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 162 through 167 removed outlier: 8.419A pdb=" N GLU E 162 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL E 157 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR E 224 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR E 185 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AB9, first strand: chain 'E' and resid 277 through 279 removed outlier: 6.095A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE E 333 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 530 through 532 removed outlier: 5.933A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP E 542 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY E 571 " --> pdb=" O ASP E 542 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL E 544 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 575 " --> pdb=" O PHE E 546 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N AMET E 474 " --> pdb=" O CYS E 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 480 through 482 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.722A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AC6, first strand: chain 'F' and resid 84 through 85 removed outlier: 4.061A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 162 through 167 removed outlier: 8.490A pdb=" N GLU F 162 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL F 157 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 226 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 347 through 348 removed outlier: 3.533A pdb=" N ARG F 332 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE F 333 " --> pdb=" O THR F 359 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA F 308 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 305 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET F 436 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 281 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'F' and resid 481 through 482 removed outlier: 3.517A pdb=" N THR F 481 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 488 " --> pdb=" O THR F 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 530 through 532 removed outlier: 3.862A pdb=" N THR F 547 " --> pdb=" O ILE F 512 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP F 542 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 544 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.934A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 12.698A pdb=" N SER G 13 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET G 12 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU G 29 " --> pdb=" O MET G 12 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS G 14 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N ASN G 27 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER G 46 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU G 29 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU G 44 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE G 40 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 35 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY G 38 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS G 84 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR G 77 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.25: 3114 1.25 - 1.42: 6486 1.42 - 1.60: 12532 1.60 - 1.77: 52 1.77 - 1.94: 224 Bond restraints: 22408 Sorted by residual: bond pdb=" C ASN G 1 " pdb=" N ASN G 2 " ideal model delta sigma weight residual 1.332 1.684 -0.352 1.40e-02 5.10e+03 6.31e+02 bond pdb=" O5' U G 0 " pdb=" C5' U G 0 " ideal model delta sigma weight residual 1.424 1.074 0.350 1.50e-02 4.44e+03 5.43e+02 bond pdb=" P U G 0 " pdb=" OP1 U G 0 " ideal model delta sigma weight residual 1.485 1.943 -0.458 2.00e-02 2.50e+03 5.25e+02 bond pdb=" C ASN G 2 " pdb=" N GLU G 3 " ideal model delta sigma weight residual 1.330 1.100 0.230 1.31e-02 5.83e+03 3.09e+02 bond pdb=" P U G 0 " pdb=" OP2 U G 0 " ideal model delta sigma weight residual 1.485 1.820 -0.335 2.00e-02 2.50e+03 2.81e+02 ... (remaining 22403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.52: 30650 5.52 - 11.04: 49 11.04 - 16.56: 4 16.56 - 22.09: 3 22.09 - 27.61: 1 Bond angle restraints: 30707 Sorted by residual: angle pdb=" CA ASN G 2 " pdb=" C ASN G 2 " pdb=" N GLU G 3 " ideal model delta sigma weight residual 116.84 89.23 27.61 1.71e+00 3.42e-01 2.61e+02 angle pdb=" N ASN G 1 " pdb=" CA ASN G 1 " pdb=" CB ASN G 1 " ideal model delta sigma weight residual 110.50 92.67 17.83 1.70e+00 3.46e-01 1.10e+02 angle pdb=" N ASN G 2 " pdb=" CA ASN G 2 " pdb=" C ASN G 2 " ideal model delta sigma weight residual 110.80 90.25 20.55 2.13e+00 2.20e-01 9.30e+01 angle pdb=" C ASN G 1 " pdb=" N ASN G 2 " pdb=" CA ASN G 2 " ideal model delta sigma weight residual 121.54 103.91 17.63 1.91e+00 2.74e-01 8.52e+01 angle pdb=" C ASN G 2 " pdb=" N GLU G 3 " pdb=" CA GLU G 3 " ideal model delta sigma weight residual 120.97 104.54 16.43 1.82e+00 3.02e-01 8.15e+01 ... (remaining 30702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.54: 12378 26.54 - 53.08: 942 53.08 - 79.62: 159 79.62 - 106.16: 15 106.16 - 132.70: 1 Dihedral angle restraints: 13495 sinusoidal: 5637 harmonic: 7858 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA THR D 84 " pdb=" C THR D 84 " pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" N ASN G 1 " pdb=" C ASN G 1 " pdb=" CA ASN G 1 " pdb=" CB ASN G 1 " ideal model delta harmonic sigma weight residual 122.80 107.92 14.88 0 2.50e+00 1.60e-01 3.54e+01 ... (remaining 13492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.538: 3563 0.538 - 1.077: 0 1.077 - 1.615: 0 1.615 - 2.154: 0 2.154 - 2.692: 1 Chirality restraints: 3564 Sorted by residual: chirality pdb=" P U G 0 " pdb=" OP1 U G 0 " pdb=" OP2 U G 0 " pdb=" O5' U G 0 " both_signs ideal model delta sigma weight residual True 2.41 -5.10 -2.69 2.00e-01 2.50e+01 1.81e+02 chirality pdb=" CA ASN G 1 " pdb=" N ASN G 1 " pdb=" C ASN G 1 " pdb=" CB ASN G 1 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASN G 2 " pdb=" N ASN G 2 " pdb=" C ASN G 2 " pdb=" CB ASN G 2 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3561 not shown) Planarity restraints: 3730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 2 " 0.055 2.00e-02 2.50e+03 1.49e-01 2.22e+02 pdb=" C ASN G 2 " -0.256 2.00e-02 2.50e+03 pdb=" O ASN G 2 " 0.106 2.00e-02 2.50e+03 pdb=" N GLU G 3 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 1 " 0.050 2.00e-02 2.50e+03 9.51e-02 9.04e+01 pdb=" C ASN G 1 " -0.164 2.00e-02 2.50e+03 pdb=" O ASN G 1 " 0.069 2.00e-02 2.50e+03 pdb=" N ASN G 2 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 694 " 0.011 2.00e-02 2.50e+03 1.91e-02 6.39e+00 pdb=" CG PHE A 694 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 694 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 694 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 694 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 694 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 694 " -0.001 2.00e-02 2.50e+03 ... (remaining 3727 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 65 2.35 - 2.99: 11473 2.99 - 3.62: 33629 3.62 - 4.26: 50360 4.26 - 4.90: 82095 Nonbonded interactions: 177622 Sorted by model distance: nonbonded pdb=" P U G 0 " pdb=" N ASN G 1 " model vdw 1.712 3.480 nonbonded pdb=" OD2 ASP A 218 " pdb="MN MN A1004 " model vdw 1.996 2.320 nonbonded pdb=" OD1 ASN A 209 " pdb="MN MN A1004 " model vdw 2.023 2.320 nonbonded pdb=" OG SER A 759 " pdb=" O2' G I 35 " model vdw 2.037 3.040 nonbonded pdb=" ND2 ASN A 209 " pdb="MN MN A1004 " model vdw 2.124 2.400 ... (remaining 177617 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 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.310 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.310 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.006 0.458 22440 Z= 0.362 Angle : 0.776 27.608 30735 Z= 0.412 Chirality : 0.062 2.692 3564 Planarity : 0.005 0.149 3730 Dihedral : 18.097 132.696 8425 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 0.53 % Allowed : 30.85 % Favored : 68.62 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.16), residues: 2638 helix: -0.26 (0.17), residues: 943 sheet: -1.64 (0.27), residues: 344 loop : -1.99 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 116 TYR 0.020 0.001 TYR A 903 PHE 0.042 0.002 PHE A 694 TRP 0.013 0.002 TRP A 916 HIS 0.006 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00638 (22408) covalent geometry : angle 0.76254 (30707) hydrogen bonds : bond 0.21463 ( 853) hydrogen bonds : angle 7.68114 ( 2357) metal coordination : bond 0.01984 ( 32) metal coordination : angle 4.83317 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.703 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: B 55 MET cc_start: 0.7447 (mmp) cc_final: 0.7069 (mmp) REVERT: B 73 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7673 (tt0) REVERT: F 106 PHE cc_start: 0.7874 (t80) cc_final: 0.7654 (t80) outliers start: 12 outliers final: 2 residues processed: 185 average time/residue: 0.1444 time to fit residues: 40.2147 Evaluate side-chains 170 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 40.0000 chunk 111 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 105 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN E 388 ASN E 559 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN F 270 GLN F 354 GLN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.203055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.149470 restraints weight = 89469.765| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 5.91 r_work: 0.3928 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22440 Z= 0.134 Angle : 0.648 11.303 30735 Z= 0.334 Chirality : 0.041 0.223 3564 Planarity : 0.004 0.060 3730 Dihedral : 12.207 128.593 3708 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 2.29 % Allowed : 28.38 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.16), residues: 2638 helix: -0.13 (0.17), residues: 976 sheet: -1.56 (0.26), residues: 374 loop : -1.85 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 10 TYR 0.019 0.001 TYR E 71 PHE 0.024 0.001 PHE E 145 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00281 (22408) covalent geometry : angle 0.63464 (30707) hydrogen bonds : bond 0.05048 ( 853) hydrogen bonds : angle 5.57679 ( 2357) metal coordination : bond 0.02002 ( 32) metal coordination : angle 4.42072 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.864 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: A 40 ASP cc_start: 0.8555 (p0) cc_final: 0.8303 (p0) REVERT: A 63 ASP cc_start: 0.7959 (t0) cc_final: 0.7743 (t0) REVERT: A 105 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7781 (ptm160) REVERT: A 110 MET cc_start: 0.7876 (mmp) cc_final: 0.7673 (mmp) REVERT: D 77 GLU cc_start: 0.8947 (tp30) cc_final: 0.8479 (tm-30) REVERT: F 106 PHE cc_start: 0.7891 (t80) cc_final: 0.7595 (t80) REVERT: F 130 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9033 (mt) REVERT: F 436 MET cc_start: 0.7078 (pmm) cc_final: 0.6859 (pmm) REVERT: G 32 TYR cc_start: 0.7428 (p90) cc_final: 0.6529 (p90) outliers start: 52 outliers final: 22 residues processed: 224 average time/residue: 0.1425 time to fit residues: 48.2742 Evaluate side-chains 191 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 262 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 599 HIS E 562 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.192835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.134569 restraints weight = 82147.446| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 6.42 r_work: 0.3832 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 22440 Z= 0.267 Angle : 0.721 13.312 30735 Z= 0.371 Chirality : 0.045 0.232 3564 Planarity : 0.005 0.062 3730 Dihedral : 12.168 130.932 3705 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.78 % Rotamer: Outliers : 4.41 % Allowed : 27.90 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.16), residues: 2638 helix: -0.36 (0.16), residues: 980 sheet: -1.67 (0.26), residues: 369 loop : -1.94 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.024 0.002 TYR A 788 PHE 0.021 0.002 PHE A 102 TRP 0.017 0.002 TRP A 916 HIS 0.007 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00617 (22408) covalent geometry : angle 0.70459 (30707) hydrogen bonds : bond 0.05619 ( 853) hydrogen bonds : angle 5.61652 ( 2357) metal coordination : bond 0.02114 ( 32) metal coordination : angle 5.17792 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 174 time to evaluate : 0.803 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: A 372 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 603 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8677 (mppt) REVERT: C 13 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8169 (tp) REVERT: F 436 MET cc_start: 0.7125 (pmm) cc_final: 0.6916 (pmm) outliers start: 100 outliers final: 54 residues processed: 256 average time/residue: 0.1334 time to fit residues: 52.8763 Evaluate side-chains 219 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 164 optimal weight: 0.1980 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 181 optimal weight: 0.2980 chunk 214 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.201096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.140204 restraints weight = 73257.135| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 5.70 r_work: 0.3909 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22440 Z= 0.135 Angle : 0.624 11.905 30735 Z= 0.320 Chirality : 0.041 0.228 3564 Planarity : 0.004 0.057 3730 Dihedral : 12.095 130.819 3705 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 3.44 % Allowed : 28.65 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.16), residues: 2638 helix: -0.05 (0.17), residues: 976 sheet: -1.60 (0.26), residues: 347 loop : -1.83 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 51 TYR 0.014 0.001 TYR B 71 PHE 0.016 0.001 PHE E 145 TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00300 (22408) covalent geometry : angle 0.60997 (30707) hydrogen bonds : bond 0.04305 ( 853) hydrogen bonds : angle 5.17980 ( 2357) metal coordination : bond 0.01660 ( 32) metal coordination : angle 4.42394 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 177 time to evaluate : 0.542 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: A 55 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7728 (ttm170) REVERT: A 603 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8556 (mppt) REVERT: E 436 MET cc_start: 0.1678 (OUTLIER) cc_final: 0.0680 (mpp) REVERT: F 106 PHE cc_start: 0.7962 (t80) cc_final: 0.7678 (t80) REVERT: F 130 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9019 (mt) REVERT: G 32 TYR cc_start: 0.7612 (p90) cc_final: 0.7352 (p90) outliers start: 78 outliers final: 48 residues processed: 241 average time/residue: 0.1395 time to fit residues: 51.5321 Evaluate side-chains 219 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 70 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 203 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.195223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.134561 restraints weight = 85757.833| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 6.47 r_work: 0.3863 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22440 Z= 0.217 Angle : 0.677 15.316 30735 Z= 0.346 Chirality : 0.043 0.230 3564 Planarity : 0.005 0.100 3730 Dihedral : 12.076 131.769 3705 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 4.89 % Allowed : 28.21 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.16), residues: 2638 helix: -0.17 (0.17), residues: 984 sheet: -1.75 (0.25), residues: 371 loop : -1.86 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 51 TYR 0.019 0.002 TYR A 788 PHE 0.019 0.002 PHE A 102 TRP 0.016 0.002 TRP A 916 HIS 0.006 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00500 (22408) covalent geometry : angle 0.65916 (30707) hydrogen bonds : bond 0.04914 ( 853) hydrogen bonds : angle 5.28859 ( 2357) metal coordination : bond 0.01971 ( 32) metal coordination : angle 5.17295 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 178 time to evaluate : 0.594 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: A 372 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8480 (mp) REVERT: A 603 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8601 (mppt) REVERT: A 889 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8165 (ttt-90) REVERT: D 94 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7587 (mtp) REVERT: E 436 MET cc_start: 0.1727 (OUTLIER) cc_final: 0.0633 (mpp) REVERT: F 106 PHE cc_start: 0.7958 (t80) cc_final: 0.7729 (t80) REVERT: F 130 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9083 (mt) REVERT: F 227 LEU cc_start: -0.1044 (OUTLIER) cc_final: -0.1271 (mt) REVERT: F 436 MET cc_start: 0.6886 (pmm) cc_final: 0.5701 (pmm) REVERT: G 58 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8270 (ttpp) outliers start: 111 outliers final: 77 residues processed: 270 average time/residue: 0.1407 time to fit residues: 58.8065 Evaluate side-chains 254 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 170 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 175 optimal weight: 30.0000 chunk 96 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.186942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.130741 restraints weight = 68976.062| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 4.95 r_work: 0.3627 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22440 Z= 0.134 Angle : 0.623 12.087 30735 Z= 0.318 Chirality : 0.041 0.227 3564 Planarity : 0.004 0.105 3730 Dihedral : 12.015 131.673 3705 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 4.01 % Allowed : 29.13 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.16), residues: 2638 helix: 0.06 (0.17), residues: 982 sheet: -1.56 (0.27), residues: 337 loop : -1.83 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 427 TYR 0.015 0.001 TYR F 224 PHE 0.014 0.001 PHE G 40 TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00300 (22408) covalent geometry : angle 0.60840 (30707) hydrogen bonds : bond 0.04089 ( 853) hydrogen bonds : angle 5.00132 ( 2357) metal coordination : bond 0.01720 ( 32) metal coordination : angle 4.47841 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 181 time to evaluate : 0.828 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: A 603 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8590 (mppt) REVERT: B 171 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: D 67 MET cc_start: 0.6248 (ttp) cc_final: 0.5808 (tmm) REVERT: E 436 MET cc_start: 0.0741 (OUTLIER) cc_final: -0.0534 (mpp) REVERT: F 106 PHE cc_start: 0.7941 (t80) cc_final: 0.7642 (t80) REVERT: F 130 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9024 (mt) REVERT: F 436 MET cc_start: 0.7200 (pmm) cc_final: 0.6191 (pmm) REVERT: G 87 TYR cc_start: 0.7397 (m-80) cc_final: 0.7177 (m-80) outliers start: 91 outliers final: 71 residues processed: 254 average time/residue: 0.1377 time to fit residues: 54.1911 Evaluate side-chains 248 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 263 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 252 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 237 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.186443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.130116 restraints weight = 68958.949| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 5.17 r_work: 0.3637 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22440 Z= 0.132 Angle : 0.622 12.548 30735 Z= 0.315 Chirality : 0.041 0.226 3564 Planarity : 0.004 0.098 3730 Dihedral : 11.932 131.676 3705 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 4.45 % Allowed : 28.91 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.16), residues: 2638 helix: 0.15 (0.17), residues: 976 sheet: -1.49 (0.27), residues: 339 loop : -1.74 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 57 TYR 0.031 0.001 TYR A 903 PHE 0.014 0.001 PHE D 92 TRP 0.013 0.001 TRP A 916 HIS 0.008 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00297 (22408) covalent geometry : angle 0.60762 (30707) hydrogen bonds : bond 0.03952 ( 853) hydrogen bonds : angle 4.89698 ( 2357) metal coordination : bond 0.01443 ( 32) metal coordination : angle 4.46406 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 180 time to evaluate : 0.794 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: A 603 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8613 (mppt) REVERT: A 643 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8752 (p) REVERT: E 32 ASP cc_start: 0.7035 (m-30) cc_final: 0.5988 (t0) REVERT: F 274 MET cc_start: 0.7720 (tmm) cc_final: 0.7477 (tmm) REVERT: F 373 PHE cc_start: 0.8694 (t80) cc_final: 0.8103 (t80) REVERT: F 436 MET cc_start: 0.7139 (pmm) cc_final: 0.6058 (pmm) REVERT: G 32 TYR cc_start: 0.7467 (p90) cc_final: 0.7238 (p90) outliers start: 101 outliers final: 74 residues processed: 265 average time/residue: 0.1305 time to fit residues: 54.2211 Evaluate side-chains 248 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 172 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 75 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 237 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.184683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.129736 restraints weight = 93524.470| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 7.00 r_work: 0.3621 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22440 Z= 0.135 Angle : 0.631 12.122 30735 Z= 0.318 Chirality : 0.041 0.225 3564 Planarity : 0.004 0.094 3730 Dihedral : 11.903 132.254 3705 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 4.10 % Allowed : 29.40 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.16), residues: 2638 helix: 0.18 (0.17), residues: 976 sheet: -1.46 (0.27), residues: 345 loop : -1.66 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 111 TYR 0.023 0.001 TYR A 903 PHE 0.026 0.001 PHE A 694 TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00305 (22408) covalent geometry : angle 0.61656 (30707) hydrogen bonds : bond 0.03890 ( 853) hydrogen bonds : angle 4.85101 ( 2357) metal coordination : bond 0.01827 ( 32) metal coordination : angle 4.47707 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 175 time to evaluate : 0.554 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: A 18 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6339 (mmm160) REVERT: A 242 MET cc_start: 0.7742 (mmp) cc_final: 0.7365 (mmp) REVERT: A 603 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8651 (mmtm) REVERT: A 643 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8692 (p) REVERT: A 889 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8209 (ttt-90) REVERT: D 39 LYS cc_start: 0.7278 (pptt) cc_final: 0.7014 (tppt) REVERT: E 32 ASP cc_start: 0.6933 (m-30) cc_final: 0.6013 (t0) REVERT: F 274 MET cc_start: 0.7800 (tmm) cc_final: 0.7547 (tmm) REVERT: F 373 PHE cc_start: 0.8745 (t80) cc_final: 0.8151 (t80) REVERT: F 436 MET cc_start: 0.7111 (pmm) cc_final: 0.6018 (pmm) outliers start: 93 outliers final: 78 residues processed: 255 average time/residue: 0.1288 time to fit residues: 50.6029 Evaluate side-chains 251 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 75 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 247 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.184140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.129919 restraints weight = 71684.736| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 5.66 r_work: 0.3612 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22440 Z= 0.147 Angle : 0.648 14.984 30735 Z= 0.324 Chirality : 0.042 0.387 3564 Planarity : 0.004 0.088 3730 Dihedral : 11.896 132.881 3705 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.88 % Rotamer: Outliers : 4.32 % Allowed : 29.26 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.16), residues: 2638 helix: 0.26 (0.17), residues: 959 sheet: -1.49 (0.27), residues: 342 loop : -1.65 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 111 TYR 0.022 0.001 TYR A 903 PHE 0.023 0.001 PHE A 694 TRP 0.013 0.001 TRP A 916 HIS 0.009 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00335 (22408) covalent geometry : angle 0.63262 (30707) hydrogen bonds : bond 0.04016 ( 853) hydrogen bonds : angle 4.88830 ( 2357) metal coordination : bond 0.01990 ( 32) metal coordination : angle 4.70819 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 174 time to evaluate : 0.765 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: A 18 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6284 (mmm160) REVERT: A 463 MET cc_start: 0.6923 (mmm) cc_final: 0.6620 (ttt) REVERT: A 603 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8674 (mmtm) REVERT: A 643 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8741 (p) REVERT: A 794 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8227 (tpt) REVERT: A 889 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8169 (ttt-90) REVERT: B 171 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: D 39 LYS cc_start: 0.7295 (pptt) cc_final: 0.7095 (tppt) REVERT: E 32 ASP cc_start: 0.6985 (m-30) cc_final: 0.6062 (t0) REVERT: E 575 ILE cc_start: 0.2557 (mm) cc_final: 0.2348 (mt) REVERT: F 274 MET cc_start: 0.7797 (tmm) cc_final: 0.7546 (tmm) REVERT: F 373 PHE cc_start: 0.8719 (t80) cc_final: 0.8122 (t80) REVERT: F 436 MET cc_start: 0.7227 (pmm) cc_final: 0.6150 (pmm) outliers start: 98 outliers final: 82 residues processed: 258 average time/residue: 0.1304 time to fit residues: 52.0606 Evaluate side-chains 258 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 170 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 221 optimal weight: 0.0020 chunk 71 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN F 107 ASN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.187017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.130863 restraints weight = 88407.199| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 6.69 r_work: 0.3627 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22440 Z= 0.118 Angle : 0.632 12.799 30735 Z= 0.315 Chirality : 0.040 0.223 3564 Planarity : 0.004 0.082 3730 Dihedral : 11.852 132.911 3705 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 3.61 % Allowed : 29.93 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.16), residues: 2638 helix: 0.38 (0.17), residues: 963 sheet: -1.28 (0.27), residues: 335 loop : -1.57 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 57 TYR 0.020 0.001 TYR A 903 PHE 0.041 0.001 PHE D 92 TRP 0.011 0.001 TRP A 916 HIS 0.010 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00262 (22408) covalent geometry : angle 0.61729 (30707) hydrogen bonds : bond 0.03578 ( 853) hydrogen bonds : angle 4.75345 ( 2357) metal coordination : bond 0.01779 ( 32) metal coordination : angle 4.56350 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 187 time to evaluate : 0.527 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: A 18 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.6139 (mmm160) REVERT: A 463 MET cc_start: 0.6849 (mmm) cc_final: 0.6577 (ttt) REVERT: A 603 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8669 (mmtm) REVERT: B 171 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: E 32 ASP cc_start: 0.7009 (m-30) cc_final: 0.6081 (t0) REVERT: F 274 MET cc_start: 0.7750 (tmm) cc_final: 0.7504 (tmm) REVERT: F 373 PHE cc_start: 0.8656 (t80) cc_final: 0.8065 (t80) REVERT: F 436 MET cc_start: 0.7359 (pmm) cc_final: 0.6358 (pmm) REVERT: G 89 TYR cc_start: 0.5703 (m-80) cc_final: 0.5363 (m-80) outliers start: 82 outliers final: 69 residues processed: 255 average time/residue: 0.1297 time to fit residues: 51.0277 Evaluate side-chains 247 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 211 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 108 optimal weight: 0.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN E 164 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.183738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.128050 restraints weight = 70833.984| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 6.07 r_work: 0.3603 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22440 Z= 0.149 Angle : 0.645 12.382 30735 Z= 0.322 Chirality : 0.041 0.224 3564 Planarity : 0.004 0.074 3730 Dihedral : 11.849 133.712 3705 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.89 % Favored : 94.00 % Rotamer: Outliers : 3.66 % Allowed : 29.93 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.16), residues: 2638 helix: 0.32 (0.17), residues: 954 sheet: -1.27 (0.28), residues: 331 loop : -1.58 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 57 TYR 0.017 0.001 TYR A 903 PHE 0.036 0.001 PHE A 694 TRP 0.012 0.001 TRP A 916 HIS 0.010 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00344 (22408) covalent geometry : angle 0.62906 (30707) hydrogen bonds : bond 0.03951 ( 853) hydrogen bonds : angle 4.82245 ( 2357) metal coordination : bond 0.01884 ( 32) metal coordination : angle 4.76744 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8974.74 seconds wall clock time: 153 minutes 7.60 seconds (9187.60 seconds total)