Starting phenix.real_space_refine on Sun Aug 24 19:43:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwe_34310/08_2025/8gwe_34310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwe_34310/08_2025/8gwe_34310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gwe_34310/08_2025/8gwe_34310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwe_34310/08_2025/8gwe_34310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwe_34310/08_2025/8gwe_34310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwe_34310/08_2025/8gwe_34310.map" } resolution = 2.66 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= 0.056 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 Zn 8 6.06 5 P 59 5.49 5 Mg 1 5.21 5 S 158 5.16 5 C 13773 2.51 5 N 3709 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 22040 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} 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: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} 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: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} 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: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} 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: 4598 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} 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: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} 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: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 1} 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: "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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 74.010 55.944 121.374 1.00 86.97 S ATOM 2506 SG CYS A 306 73.924 57.513 124.866 1.00 84.94 S ATOM 2538 SG CYS A 310 75.252 53.943 124.349 1.00 84.77 S ATOM 3946 SG CYS A 487 76.855 69.911 105.523 1.00 95.87 S ATOM 5199 SG CYS A 645 75.990 71.996 108.628 1.00 97.77 S ATOM 5205 SG CYS A 646 74.701 68.365 108.300 1.00 89.00 S ATOM 12129 SG CYS F 16 102.081 64.912 50.430 1.00183.45 S ATOM 12144 SG CYS F 19 102.885 62.214 47.803 1.00198.14 S ATOM 12047 SG CYS F 5 114.520 66.178 50.446 1.00183.01 S ATOM 12068 SG CYS F 8 115.421 69.014 48.061 1.00185.13 S ATOM 12206 SG CYS F 26 114.163 69.955 51.229 1.00172.26 S ATOM 12223 SG CYS F 29 111.697 68.063 48.813 1.00175.19 S ATOM 12388 SG CYS F 50 92.397 76.627 65.278 1.00158.72 S ATOM 12418 SG CYS F 55 89.031 75.788 63.769 1.00164.97 S ATOM 12551 SG CYS F 72 91.212 78.134 62.012 1.00168.17 S ATOM 16642 SG CYS E 16 60.616 74.147 64.663 1.00165.58 S ATOM 16657 SG CYS E 19 58.067 71.611 63.331 1.00179.24 S ATOM 16560 SG CYS E 5 69.667 70.043 57.202 1.00188.71 S ATOM 16581 SG CYS E 8 70.434 71.978 54.105 1.00197.10 S ATOM 16719 SG CYS E 26 71.793 73.436 57.435 1.00186.39 S ATOM 16736 SG CYS E 29 68.202 73.571 56.240 1.00167.57 S ATOM 16901 SG CYS E 50 65.154 87.126 78.624 1.00176.08 S ATOM 16931 SG CYS E 55 61.889 88.599 79.985 1.00192.48 S ATOM 17064 SG CYS E 72 63.981 90.622 77.488 1.00187.74 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 Time building chain proxies: 6.57, per 1000 atoms: 0.30 Number of scatterers: 22040 At special positions: 0 Unit cell: (154.56, 137.28, 187.2, 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 S 158 16.00 P 59 15.00 Mg 1 11.99 O 4332 8.00 N 3709 7.00 C 13773 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: 1.91 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 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=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " 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 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " 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 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 30 sheets defined 39.9% alpha, 10.4% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.973A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.692A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.649A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.622A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.629A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.527A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.864A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.569A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.556A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.615A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.645A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.554A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.504A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.154A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.621A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.866A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.610A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.032A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.588A pdb=" N SER A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.572A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.585A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.526A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.504A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.792A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.581A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.387A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.676A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.606A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 11 through 28 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.644A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.764A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.619A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 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 removed outlier: 3.664A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.680A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 80 removed outlier: 3.886A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.843A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.570A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.231A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 Processing helix chain 'F' and resid 265 through 275 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.684A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 381 through 391 removed outlier: 3.632A pdb=" N LEU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 removed outlier: 3.998A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.616A pdb=" N VAL F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.912A pdb=" N TRP F 506 " --> pdb=" O ASN F 503 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 516 through 523 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.093A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.748A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.508A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.863A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.497A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'E' and resid 494 through 500 Processing helix chain 'E' and resid 505 through 509 removed outlier: 4.423A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 509 " --> pdb=" O TRP E 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 505 through 509' Processing helix chain 'E' and resid 515 through 526 Processing helix chain 'E' and resid 560 through 565 removed outlier: 4.016A pdb=" N ALA E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) 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: 5.374A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.689A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.552A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.552A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.971A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (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 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.344A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AB3, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AB6, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AB7, first strand: chain 'F' and resid 200 through 202 Processing sheet with id=AB8, first strand: chain 'F' and resid 304 through 305 removed outlier: 5.091A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 330 through 331 removed outlier: 3.532A pdb=" N SER F 331 " --> pdb=" O TYR F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC3, first strand: chain 'E' and resid 24 through 25 removed outlier: 4.433A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AC5, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.672A pdb=" N PHE E 225 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 187 removed outlier: 6.958A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 195 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.593A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 481 through 482 removed outlier: 3.854A pdb=" N THR E 481 " --> pdb=" O ILE E 488 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 511 through 512 removed outlier: 6.087A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 544 through 546 removed outlier: 3.552A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.738A pdb=" N ALA G 54 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.534A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.45 - 0.72: 1 0.72 - 1.00: 0 1.00 - 1.27: 3475 1.27 - 1.54: 18728 1.54 - 1.82: 416 Warning: very small bond lengths. Bond restraints: 22620 Sorted by residual: bond pdb=" CG PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.503 0.446 1.057 3.40e-02 8.65e+02 9.66e+02 bond pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.473 1.631 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" CA ASN G 2 " pdb=" C ASN G 2 " ideal model delta sigma weight residual 1.526 1.437 0.089 1.20e-02 6.94e+03 5.50e+01 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.265 0.238 3.40e-02 8.65e+02 4.90e+01 bond pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.73e+01 ... (remaining 22615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.80: 30948 6.80 - 13.61: 57 13.61 - 20.41: 9 20.41 - 27.22: 5 27.22 - 34.02: 2 Bond angle restraints: 31021 Sorted by residual: angle pdb=" N PRO F 491 " pdb=" CD PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 103.20 69.18 34.02 1.50e+00 4.44e-01 5.14e+02 angle pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 112.00 89.92 22.08 1.40e+00 5.10e-01 2.49e+02 angle pdb=" CA PRO F 491 " pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 112.00 90.70 21.30 1.40e+00 5.10e-01 2.32e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.72 -27.92 2.13e+00 2.20e-01 1.72e+02 angle pdb=" CA PRO F 491 " pdb=" CB PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 104.50 80.62 23.88 1.90e+00 2.77e-01 1.58e+02 ... (remaining 31016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.39: 11629 19.39 - 38.79: 1456 38.79 - 58.18: 451 58.18 - 77.57: 86 77.57 - 96.97: 15 Dihedral angle restraints: 13637 sinusoidal: 5743 harmonic: 7894 Sorted by residual: dihedral pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual 122.80 159.42 -36.62 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" C CYS G 14 " pdb=" N CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual -122.60 -158.50 35.90 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual 122.80 147.55 -24.75 0 2.50e+00 1.60e-01 9.80e+01 ... (remaining 13634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3593 0.321 - 0.642: 4 0.642 - 0.963: 0 0.963 - 1.283: 2 1.283 - 1.604: 2 Chirality restraints: 3601 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.60 2.00e-01 2.50e+01 6.43e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.45e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.61e+01 ... (remaining 3598 not shown) Planarity restraints: 3752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 1 " -0.046 2.00e-02 2.50e+03 8.33e-02 6.93e+01 pdb=" C ASN G 1 " 0.144 2.00e-02 2.50e+03 pdb=" O ASN G 1 " -0.051 2.00e-02 2.50e+03 pdb=" N ASN G 2 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.107 5.00e-02 4.00e+02 1.40e-01 3.16e+01 pdb=" N PRO E 364 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.091 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO F 491 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3749 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 4 1.83 - 2.60: 263 2.60 - 3.37: 27687 3.37 - 4.13: 52833 4.13 - 4.90: 93860 Nonbonded interactions: 174647 Sorted by model distance: nonbonded pdb=" O2G GNP A1003 " pdb="MG MG H 101 " model vdw 1.065 2.170 nonbonded pdb=" PG GNP A1003 " pdb="MG MG H 101 " model vdw 1.486 2.530 nonbonded pdb=" O1G GNP A1003 " pdb="MG MG H 101 " model vdw 1.591 2.170 nonbonded pdb=" N ASN G 1 " pdb=" P A H 1 " model vdw 1.597 3.480 nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 3.040 ... (remaining 174642 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 192)) 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 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 1 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=0.11 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: 5.800 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 26.660 Find NCS groups from input model: 0.270 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0955 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 : 0.009 1.057 22652 Z= 0.349 Angle : 0.984 34.024 31048 Z= 0.555 Chirality : 0.063 1.604 3601 Planarity : 0.006 0.140 3752 Dihedral : 18.803 96.966 8543 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.43 % Favored : 91.23 % Rotamer: Outliers : 5.00 % Allowed : 33.63 % Favored : 61.37 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 946 sheet: -1.48 (0.35), residues: 217 loop : -2.47 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 22 TYR 0.021 0.001 TYR F 299 PHE 0.017 0.001 PHE F 437 TRP 0.038 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00879 (22620) covalent geometry : angle 0.97279 (31021) hydrogen bonds : bond 0.18410 ( 842) hydrogen bonds : angle 6.40337 ( 2324) metal coordination : bond 0.01929 ( 32) metal coordination : angle 5.21557 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 279 time to evaluate : 0.772 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 77 PHE cc_start: 0.1025 (t80) cc_final: 0.0600 (p90) REVERT: A 162 TRP cc_start: 0.0416 (p-90) cc_final: -0.0721 (p-90) REVERT: A 226 THR cc_start: 0.7061 (p) cc_final: 0.6840 (t) REVERT: A 235 ASP cc_start: 0.1665 (OUTLIER) cc_final: 0.0797 (m-30) REVERT: A 566 MET cc_start: 0.3252 (ttm) cc_final: 0.2293 (mmt) REVERT: B 51 ARG cc_start: 0.1916 (mpp-170) cc_final: 0.1536 (tpp80) REVERT: B 114 CYS cc_start: -0.0518 (OUTLIER) cc_final: -0.1070 (m) REVERT: B 155 GLU cc_start: 0.3755 (pt0) cc_final: 0.3224 (mp0) REVERT: D 70 MET cc_start: 0.0397 (ptm) cc_final: -0.0287 (mtt) REVERT: D 139 LYS cc_start: 0.7135 (ttpp) cc_final: 0.6747 (tppt) REVERT: D 140 ASN cc_start: 0.6397 (m-40) cc_final: 0.6004 (t0) REVERT: D 146 THR cc_start: 0.1462 (p) cc_final: 0.1218 (t) REVERT: D 185 ILE cc_start: 0.2302 (OUTLIER) cc_final: 0.2079 (pt) REVERT: F 40 LYS cc_start: 0.6223 (ttmm) cc_final: 0.5728 (tppp) REVERT: F 80 SER cc_start: -0.0327 (OUTLIER) cc_final: -0.2667 (t) REVERT: F 122 LEU cc_start: 0.6175 (tt) cc_final: 0.5678 (mt) REVERT: F 453 SER cc_start: 0.1539 (OUTLIER) cc_final: 0.1137 (p) REVERT: F 495 VAL cc_start: -0.0711 (OUTLIER) cc_final: -0.0940 (p) REVERT: F 532 THR cc_start: 0.1472 (OUTLIER) cc_final: 0.1064 (t) REVERT: F 576 MET cc_start: -0.1261 (mmt) cc_final: -0.1575 (pp-130) REVERT: E 73 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7612 (tmmt) REVERT: E 183 THR cc_start: 0.4608 (OUTLIER) cc_final: 0.4181 (p) REVERT: E 233 MET cc_start: -0.2863 (mpm) cc_final: -0.4470 (tpt) REVERT: E 248 ARG cc_start: 0.6032 (mtt180) cc_final: 0.5662 (mmm-85) REVERT: E 280 LEU cc_start: 0.3714 (mt) cc_final: 0.3462 (tm) REVERT: G 10 ARG cc_start: 0.2455 (OUTLIER) cc_final: 0.1548 (tpm170) REVERT: G 73 CYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5222 (p) outliers start: 113 outliers final: 20 residues processed: 382 average time/residue: 0.4398 time to fit residues: 200.8798 Evaluate side-chains 199 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 213 ASN A 312 ASN A 492 GLN A 534 ASN A 572 HIS A 611 ASN A 705 ASN A 790 ASN ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN A 911 ASN C 19 GLN D 176 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 230 HIS ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.227360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.167080 restraints weight = 79117.355| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 5.30 r_work: 0.4042 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1636 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 22652 Z= 0.237 Angle : 0.902 16.231 31048 Z= 0.455 Chirality : 0.049 0.343 3601 Planarity : 0.006 0.070 3752 Dihedral : 13.134 86.769 3843 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.30 % Favored : 90.43 % Rotamer: Outliers : 6.80 % Allowed : 30.68 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.15), residues: 2650 helix: -0.27 (0.17), residues: 956 sheet: -1.49 (0.34), residues: 222 loop : -2.56 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 155 TYR 0.049 0.003 TYR A 129 PHE 0.037 0.003 PHE A 348 TRP 0.030 0.003 TRP A 216 HIS 0.019 0.002 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00482 (22620) covalent geometry : angle 0.88493 (31021) hydrogen bonds : bond 0.06036 ( 842) hydrogen bonds : angle 5.77909 ( 2324) metal coordination : bond 0.02788 ( 32) metal coordination : angle 6.01784 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 192 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.4197 (OUTLIER) cc_final: 0.3927 (pt0) REVERT: A 217 TYR cc_start: 0.2439 (p90) cc_final: 0.2013 (p90) REVERT: A 226 THR cc_start: 0.7703 (p) cc_final: 0.7318 (t) REVERT: A 566 MET cc_start: 0.4229 (ttm) cc_final: 0.3481 (mmt) REVERT: A 633 MET cc_start: 0.0756 (ttp) cc_final: -0.1432 (mpp) REVERT: A 666 MET cc_start: -0.0209 (OUTLIER) cc_final: -0.1184 (pmm) REVERT: A 883 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4500 (mt) REVERT: C 68 ILE cc_start: -0.2916 (OUTLIER) cc_final: -0.3380 (mm) REVERT: D 42 LEU cc_start: 0.0392 (OUTLIER) cc_final: 0.0133 (mt) REVERT: D 70 MET cc_start: 0.0897 (ptm) cc_final: -0.0546 (mtp) REVERT: D 139 LYS cc_start: 0.7257 (ttpp) cc_final: 0.6810 (tppt) REVERT: D 140 ASN cc_start: 0.6485 (m-40) cc_final: 0.5991 (t0) REVERT: D 182 TRP cc_start: -0.0582 (OUTLIER) cc_final: -0.1503 (m100) REVERT: F 122 LEU cc_start: 0.6314 (tt) cc_final: 0.5804 (mt) REVERT: F 128 GLU cc_start: 0.3080 (tp30) cc_final: 0.2828 (mm-30) REVERT: F 162 GLU cc_start: 0.7528 (pp20) cc_final: 0.7089 (mp0) REVERT: F 185 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6807 (p90) REVERT: F 493 ILE cc_start: -0.0035 (OUTLIER) cc_final: -0.0347 (tp) REVERT: E 68 MET cc_start: 0.0509 (OUTLIER) cc_final: -0.1006 (pp-130) REVERT: E 198 TYR cc_start: 0.4130 (OUTLIER) cc_final: 0.3687 (m-80) REVERT: E 233 MET cc_start: -0.2963 (OUTLIER) cc_final: -0.4523 (tpt) REVERT: E 270 GLN cc_start: 0.7158 (tt0) cc_final: 0.6537 (mp10) REVERT: E 280 LEU cc_start: 0.4046 (mt) cc_final: 0.3815 (tm) REVERT: E 315 ASP cc_start: 0.4410 (OUTLIER) cc_final: 0.3982 (t0) REVERT: E 578 ASP cc_start: 0.1023 (OUTLIER) cc_final: -0.0056 (p0) REVERT: E 579 ARG cc_start: 0.4325 (tpp-160) cc_final: 0.4071 (tpp-160) REVERT: G 10 ARG cc_start: 0.2696 (OUTLIER) cc_final: 0.2156 (mmp80) REVERT: G 33 ASN cc_start: 0.5519 (t0) cc_final: 0.5313 (t0) outliers start: 154 outliers final: 49 residues processed: 320 average time/residue: 0.4557 time to fit residues: 172.3396 Evaluate side-chains 222 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 33 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 0.0570 chunk 28 optimal weight: 0.0070 chunk 84 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 chunk 248 optimal weight: 20.0000 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 464 HIS ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** 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 = 0.4840 r_free = 0.4840 target = 0.227360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.162156 restraints weight = 75469.850| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 4.13 r_work: 0.4024 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1532 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22652 Z= 0.133 Angle : 0.695 16.084 31048 Z= 0.347 Chirality : 0.043 0.279 3601 Planarity : 0.005 0.103 3752 Dihedral : 12.587 83.042 3821 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.41 % Favored : 92.32 % Rotamer: Outliers : 4.39 % Allowed : 32.84 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.16), residues: 2650 helix: 0.03 (0.17), residues: 975 sheet: -0.99 (0.35), residues: 225 loop : -2.35 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 560 TYR 0.022 0.001 TYR F 476 PHE 0.019 0.001 PHE E 422 TRP 0.029 0.001 TRP B 182 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00276 (22620) covalent geometry : angle 0.68188 (31021) hydrogen bonds : bond 0.04738 ( 842) hydrogen bonds : angle 5.16762 ( 2324) metal coordination : bond 0.01851 ( 32) metal coordination : angle 4.57681 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 176 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TRP cc_start: 0.1216 (p-90) cc_final: -0.0547 (p-90) REVERT: A 226 THR cc_start: 0.7620 (p) cc_final: 0.7218 (t) REVERT: A 615 MET cc_start: -0.0481 (OUTLIER) cc_final: -0.0743 (tpt) REVERT: A 633 MET cc_start: 0.0817 (ttp) cc_final: -0.1377 (mpp) REVERT: A 666 MET cc_start: 0.0014 (OUTLIER) cc_final: -0.0536 (pmm) REVERT: A 875 GLN cc_start: 0.2709 (mp10) cc_final: 0.2454 (mt0) REVERT: A 883 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.4800 (mt) REVERT: B 79 LYS cc_start: 0.0652 (pttt) cc_final: 0.0238 (mtmt) REVERT: C 14 LEU cc_start: 0.0139 (OUTLIER) cc_final: -0.0062 (tp) REVERT: D 42 LEU cc_start: 0.0499 (OUTLIER) cc_final: 0.0155 (mt) REVERT: D 70 MET cc_start: 0.0810 (ptm) cc_final: -0.0409 (mtp) REVERT: D 139 LYS cc_start: 0.7175 (ttpp) cc_final: 0.6775 (tppt) REVERT: D 140 ASN cc_start: 0.6506 (m-40) cc_final: 0.5877 (t0) REVERT: D 182 TRP cc_start: -0.0612 (OUTLIER) cc_final: -0.1657 (m100) REVERT: F 122 LEU cc_start: 0.6252 (tt) cc_final: 0.5782 (mt) REVERT: F 185 TYR cc_start: 0.7211 (p90) cc_final: 0.6689 (p90) REVERT: F 493 ILE cc_start: -0.0033 (OUTLIER) cc_final: -0.0341 (tp) REVERT: E 12 THR cc_start: -0.1274 (OUTLIER) cc_final: -0.1746 (t) REVERT: E 32 ASP cc_start: 0.5096 (m-30) cc_final: 0.4200 (t70) REVERT: E 68 MET cc_start: 0.0412 (OUTLIER) cc_final: -0.1087 (pp-130) REVERT: E 155 ARG cc_start: 0.1461 (mmt180) cc_final: 0.0615 (tpp80) REVERT: E 233 MET cc_start: -0.2862 (mpm) cc_final: -0.4311 (tpt) REVERT: E 270 GLN cc_start: 0.7166 (tt0) cc_final: 0.6491 (mp10) REVERT: E 280 LEU cc_start: 0.3766 (mt) cc_final: 0.3119 (tp) REVERT: E 315 ASP cc_start: 0.4456 (OUTLIER) cc_final: 0.4020 (t0) REVERT: E 350 SER cc_start: -0.0383 (OUTLIER) cc_final: -0.1047 (m) REVERT: G 10 ARG cc_start: 0.2608 (OUTLIER) cc_final: 0.1689 (tpp-160) REVERT: G 11 GLN cc_start: 0.0366 (OUTLIER) cc_final: -0.0005 (mp10) REVERT: G 88 LEU cc_start: 0.3619 (OUTLIER) cc_final: 0.2405 (pp) REVERT: G 89 TYR cc_start: 0.1315 (m-80) cc_final: 0.0925 (m-80) outliers start: 99 outliers final: 35 residues processed: 255 average time/residue: 0.4953 time to fit residues: 150.7390 Evaluate side-chains 210 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 81 PHE Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 252 optimal weight: 20.0000 chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 447 ASN A 492 GLN A 650 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 GLN G 1 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.233614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.176881 restraints weight = 81177.868| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 4.50 r_work: 0.4145 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4122 r_free = 0.4122 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4122 r_free = 0.4122 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2042 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22652 Z= 0.199 Angle : 0.803 15.633 31048 Z= 0.403 Chirality : 0.046 0.260 3601 Planarity : 0.006 0.058 3752 Dihedral : 12.688 85.019 3818 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.74 % Favored : 91.04 % Rotamer: Outliers : 5.66 % Allowed : 31.30 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.16), residues: 2650 helix: -0.36 (0.16), residues: 961 sheet: -1.07 (0.36), residues: 220 loop : -2.40 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 560 TYR 0.054 0.003 TYR F 476 PHE 0.037 0.003 PHE A 348 TRP 0.031 0.002 TRP B 182 HIS 0.013 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00426 (22620) covalent geometry : angle 0.79313 (31021) hydrogen bonds : bond 0.05348 ( 842) hydrogen bonds : angle 5.57798 ( 2324) metal coordination : bond 0.02017 ( 32) metal coordination : angle 4.22540 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 180 time to evaluate : 0.857 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 113 HIS cc_start: 0.1925 (OUTLIER) cc_final: 0.1284 (m170) REVERT: A 226 THR cc_start: 0.7998 (p) cc_final: 0.7570 (t) REVERT: A 242 MET cc_start: 0.2284 (OUTLIER) cc_final: 0.1245 (mtp) REVERT: A 633 MET cc_start: 0.1911 (ttp) cc_final: -0.0658 (mpp) REVERT: A 666 MET cc_start: 0.0720 (OUTLIER) cc_final: -0.0340 (pmm) REVERT: A 775 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.1512 (pt) REVERT: A 778 SER cc_start: -0.1686 (OUTLIER) cc_final: -0.1919 (t) REVERT: A 835 SER cc_start: 0.8267 (t) cc_final: 0.7948 (p) REVERT: A 871 LYS cc_start: 0.2644 (mppt) cc_final: 0.1624 (tmtt) REVERT: A 883 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.4237 (mt) REVERT: C 68 ILE cc_start: -0.2703 (OUTLIER) cc_final: -0.3024 (mm) REVERT: D 42 LEU cc_start: -0.0117 (OUTLIER) cc_final: -0.0543 (mt) REVERT: D 67 MET cc_start: -0.0564 (ttt) cc_final: -0.1777 (ptp) REVERT: D 70 MET cc_start: 0.1051 (ptm) cc_final: -0.0593 (mtt) REVERT: D 139 LYS cc_start: 0.7155 (ttpp) cc_final: 0.6781 (tppt) REVERT: D 140 ASN cc_start: 0.6452 (m-40) cc_final: 0.5753 (t0) REVERT: D 182 TRP cc_start: -0.0440 (OUTLIER) cc_final: -0.1526 (m100) REVERT: F 75 HIS cc_start: -0.0606 (OUTLIER) cc_final: -0.2729 (t-90) REVERT: F 93 TYR cc_start: -0.0026 (m-80) cc_final: -0.1441 (t80) REVERT: F 122 LEU cc_start: 0.6311 (tt) cc_final: 0.5804 (mt) REVERT: F 185 TYR cc_start: 0.7320 (p90) cc_final: 0.6707 (p90) REVERT: F 289 SER cc_start: 0.1367 (OUTLIER) cc_final: 0.1061 (p) REVERT: F 526 LEU cc_start: -0.0298 (OUTLIER) cc_final: -0.0634 (pp) REVERT: F 551 GLU cc_start: -0.0661 (pt0) cc_final: -0.2100 (pm20) REVERT: E 12 THR cc_start: -0.1799 (OUTLIER) cc_final: -0.2058 (t) REVERT: E 32 ASP cc_start: 0.5023 (m-30) cc_final: 0.4221 (t70) REVERT: E 233 MET cc_start: -0.2771 (OUTLIER) cc_final: -0.4510 (tpt) REVERT: E 270 GLN cc_start: 0.7217 (tt0) cc_final: 0.6634 (mp10) REVERT: E 280 LEU cc_start: 0.3323 (mt) cc_final: 0.2763 (tp) REVERT: E 315 ASP cc_start: 0.4449 (OUTLIER) cc_final: 0.4070 (t0) REVERT: E 350 SER cc_start: -0.0193 (OUTLIER) cc_final: -0.0822 (m) REVERT: E 429 MET cc_start: 0.0425 (OUTLIER) cc_final: 0.0214 (ttp) REVERT: E 578 ASP cc_start: 0.1125 (OUTLIER) cc_final: 0.0606 (p0) REVERT: G 3 GLU cc_start: 0.1237 (OUTLIER) cc_final: -0.0652 (mm-30) REVERT: G 10 ARG cc_start: 0.2478 (OUTLIER) cc_final: 0.1454 (tpp-160) outliers start: 128 outliers final: 52 residues processed: 280 average time/residue: 0.4851 time to fit residues: 162.2738 Evaluate side-chains 237 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 1 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 205 optimal weight: 0.0010 chunk 262 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 167 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 chunk 45 optimal weight: 0.2980 chunk 129 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 886 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.233969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.176661 restraints weight = 78202.609| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 4.51 r_work: 0.4167 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1917 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22652 Z= 0.127 Angle : 0.674 14.726 31048 Z= 0.336 Chirality : 0.042 0.331 3601 Planarity : 0.005 0.050 3752 Dihedral : 12.369 82.318 3817 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.68 % Favored : 92.10 % Rotamer: Outliers : 4.08 % Allowed : 33.32 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.16), residues: 2650 helix: -0.08 (0.17), residues: 973 sheet: -0.92 (0.37), residues: 218 loop : -2.27 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 560 TYR 0.051 0.002 TYR F 476 PHE 0.017 0.001 PHE A 348 TRP 0.023 0.002 TRP A 598 HIS 0.013 0.001 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00269 (22620) covalent geometry : angle 0.66549 (31021) hydrogen bonds : bond 0.04516 ( 842) hydrogen bonds : angle 5.10531 ( 2324) metal coordination : bond 0.01714 ( 32) metal coordination : angle 3.75961 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 166 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 THR cc_start: 0.7808 (p) cc_final: 0.7418 (t) REVERT: A 239 SER cc_start: 0.1412 (OUTLIER) cc_final: 0.1124 (t) REVERT: A 242 MET cc_start: 0.1848 (OUTLIER) cc_final: 0.1076 (mtt) REVERT: A 471 PHE cc_start: 0.4677 (p90) cc_final: 0.1318 (t80) REVERT: A 633 MET cc_start: 0.1952 (ttp) cc_final: -0.0636 (mpp) REVERT: A 871 LYS cc_start: 0.2435 (mppt) cc_final: 0.1450 (tmtt) REVERT: A 875 GLN cc_start: 0.3084 (mp10) cc_final: 0.2774 (mt0) REVERT: A 909 ASN cc_start: 0.4368 (t0) cc_final: 0.2633 (m110) REVERT: B 79 LYS cc_start: 0.0587 (pttt) cc_final: 0.0079 (mtmt) REVERT: C 68 ILE cc_start: -0.2570 (OUTLIER) cc_final: -0.2782 (mm) REVERT: D 42 LEU cc_start: 0.0021 (OUTLIER) cc_final: -0.0427 (mt) REVERT: D 70 MET cc_start: 0.0723 (ptm) cc_final: -0.0607 (mtt) REVERT: D 87 MET cc_start: 0.0432 (tpp) cc_final: -0.0108 (mmt) REVERT: D 139 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6920 (tppt) REVERT: D 182 TRP cc_start: -0.0188 (OUTLIER) cc_final: -0.1330 (m100) REVERT: F 93 TYR cc_start: -0.0075 (m-80) cc_final: -0.1502 (m-80) REVERT: F 122 LEU cc_start: 0.6283 (tt) cc_final: 0.5799 (mt) REVERT: F 185 TYR cc_start: 0.7239 (p90) cc_final: 0.6759 (p90) REVERT: F 248 ARG cc_start: 0.4854 (tmm160) cc_final: 0.4075 (tpm170) REVERT: F 289 SER cc_start: 0.1302 (OUTLIER) cc_final: 0.1006 (p) REVERT: F 526 LEU cc_start: -0.0309 (OUTLIER) cc_final: -0.0665 (pp) REVERT: F 551 GLU cc_start: -0.0763 (pt0) cc_final: -0.1915 (pm20) REVERT: E 32 ASP cc_start: 0.5007 (m-30) cc_final: 0.4335 (t70) REVERT: E 68 MET cc_start: 0.0197 (OUTLIER) cc_final: -0.1137 (pp-130) REVERT: E 73 LYS cc_start: 0.8328 (mppt) cc_final: 0.7927 (ttpp) REVERT: E 233 MET cc_start: -0.2794 (mpm) cc_final: -0.4157 (tpt) REVERT: E 270 GLN cc_start: 0.7100 (tt0) cc_final: 0.6600 (mp10) REVERT: E 280 LEU cc_start: 0.3276 (mt) cc_final: 0.2659 (tp) REVERT: E 315 ASP cc_start: 0.4120 (OUTLIER) cc_final: 0.3835 (t0) REVERT: E 350 SER cc_start: 0.0072 (OUTLIER) cc_final: -0.0559 (m) REVERT: E 351 THR cc_start: 0.4351 (OUTLIER) cc_final: 0.4081 (t) REVERT: E 420 GLU cc_start: 0.5702 (mp0) cc_final: 0.5401 (mp0) REVERT: E 436 MET cc_start: 0.0599 (pp-130) cc_final: 0.0290 (pp-130) REVERT: E 497 ARG cc_start: 0.4145 (OUTLIER) cc_final: 0.3941 (mmt90) REVERT: E 578 ASP cc_start: 0.0947 (OUTLIER) cc_final: 0.0480 (p0) REVERT: G 3 GLU cc_start: 0.1071 (OUTLIER) cc_final: -0.0649 (mm-30) REVERT: G 10 ARG cc_start: 0.2291 (OUTLIER) cc_final: 0.1470 (tpp-160) REVERT: G 33 ASN cc_start: 0.4943 (t0) cc_final: 0.4688 (t0) outliers start: 92 outliers final: 43 residues processed: 237 average time/residue: 0.4886 time to fit residues: 137.9872 Evaluate side-chains 216 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 158 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 214 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 459 ASN A 492 GLN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN A 886 GLN B 118 ASN C 78 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.242105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.195871 restraints weight = 74750.882| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 4.40 r_work: 0.4399 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2448 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 22652 Z= 0.263 Angle : 0.941 19.335 31048 Z= 0.471 Chirality : 0.050 0.283 3601 Planarity : 0.006 0.065 3752 Dihedral : 12.904 86.748 3817 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.95 % Favored : 89.86 % Rotamer: Outliers : 5.79 % Allowed : 32.13 % Favored : 62.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.15), residues: 2650 helix: -0.86 (0.16), residues: 960 sheet: -1.31 (0.35), residues: 223 loop : -2.53 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 889 TYR 0.045 0.003 TYR A 237 PHE 0.050 0.004 PHE A 843 TRP 0.022 0.003 TRP A 800 HIS 0.014 0.002 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00577 (22620) covalent geometry : angle 0.92165 (31021) hydrogen bonds : bond 0.06392 ( 842) hydrogen bonds : angle 6.25622 ( 2324) metal coordination : bond 0.03673 ( 32) metal coordination : angle 6.52649 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 175 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2572 (OUTLIER) cc_final: 0.0916 (m170) REVERT: A 242 MET cc_start: 0.2023 (OUTLIER) cc_final: 0.0282 (mtp) REVERT: A 482 CYS cc_start: 0.2944 (OUTLIER) cc_final: 0.2246 (t) REVERT: A 566 MET cc_start: 0.2832 (mmt) cc_final: 0.1946 (mtt) REVERT: A 633 MET cc_start: 0.2080 (ttp) cc_final: -0.0527 (mpt) REVERT: A 666 MET cc_start: 0.0287 (OUTLIER) cc_final: -0.0929 (ptp) REVERT: A 770 TYR cc_start: -0.0557 (OUTLIER) cc_final: -0.1185 (m-80) REVERT: A 822 GLN cc_start: 0.0299 (OUTLIER) cc_final: -0.3648 (mm-40) REVERT: A 871 LYS cc_start: 0.2456 (mppt) cc_final: 0.1516 (mppt) REVERT: A 889 ARG cc_start: 0.7163 (ttp80) cc_final: 0.6651 (ttm110) REVERT: B 79 LYS cc_start: 0.0952 (pttt) cc_final: 0.0148 (mtmt) REVERT: B 129 MET cc_start: 0.0153 (ttp) cc_final: -0.0159 (ttp) REVERT: B 147 PHE cc_start: 0.3565 (p90) cc_final: 0.2945 (p90) REVERT: C 52 MET cc_start: 0.5550 (mmm) cc_final: 0.5089 (mmm) REVERT: D 70 MET cc_start: 0.1588 (ptm) cc_final: -0.0570 (mtt) REVERT: D 87 MET cc_start: 0.1168 (tpp) cc_final: 0.0495 (tpp) REVERT: D 182 TRP cc_start: 0.0345 (OUTLIER) cc_final: -0.0977 (m100) REVERT: F 57 VAL cc_start: -0.1966 (OUTLIER) cc_final: -0.2239 (m) REVERT: F 75 HIS cc_start: -0.0805 (OUTLIER) cc_final: -0.3184 (t-90) REVERT: F 93 TYR cc_start: -0.0171 (m-80) cc_final: -0.1867 (t80) REVERT: F 122 LEU cc_start: 0.6353 (tt) cc_final: 0.5955 (mt) REVERT: F 131 LYS cc_start: -0.0815 (OUTLIER) cc_final: -0.1260 (tptt) REVERT: F 162 GLU cc_start: 0.7400 (pp20) cc_final: 0.6973 (pm20) REVERT: F 185 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6843 (p90) REVERT: F 248 ARG cc_start: 0.4776 (OUTLIER) cc_final: 0.3969 (tpm170) REVERT: F 289 SER cc_start: 0.1105 (OUTLIER) cc_final: 0.0852 (p) REVERT: F 391 LEU cc_start: 0.3930 (OUTLIER) cc_final: 0.3467 (mm) REVERT: F 526 LEU cc_start: -0.0306 (OUTLIER) cc_final: -0.0650 (pp) REVERT: F 551 GLU cc_start: -0.0488 (pt0) cc_final: -0.1919 (pm20) REVERT: E 32 ASP cc_start: 0.5041 (m-30) cc_final: 0.4147 (t70) REVERT: E 68 MET cc_start: 0.0674 (OUTLIER) cc_final: -0.0423 (pp-130) REVERT: E 198 TYR cc_start: 0.4351 (OUTLIER) cc_final: 0.3885 (m-80) REVERT: E 233 MET cc_start: -0.2130 (OUTLIER) cc_final: -0.3945 (tpt) REVERT: E 270 GLN cc_start: 0.7003 (tt0) cc_final: 0.6485 (mp10) REVERT: E 280 LEU cc_start: 0.3024 (mt) cc_final: 0.2453 (tm) REVERT: E 306 TYR cc_start: 0.3388 (m-80) cc_final: 0.2966 (m-80) REVERT: E 315 ASP cc_start: 0.4135 (OUTLIER) cc_final: 0.3864 (t0) REVERT: E 350 SER cc_start: 0.0405 (OUTLIER) cc_final: -0.0231 (m) REVERT: E 351 THR cc_start: 0.4499 (OUTLIER) cc_final: 0.4243 (t) REVERT: E 497 ARG cc_start: 0.3978 (OUTLIER) cc_final: 0.3742 (mmt90) REVERT: E 578 ASP cc_start: 0.0882 (OUTLIER) cc_final: 0.0428 (p0) REVERT: G 3 GLU cc_start: 0.1058 (OUTLIER) cc_final: -0.0636 (mm-30) REVERT: G 10 ARG cc_start: 0.2216 (OUTLIER) cc_final: 0.1472 (tpm170) REVERT: G 33 ASN cc_start: 0.5063 (t0) cc_final: 0.4767 (t0) outliers start: 131 outliers final: 51 residues processed: 281 average time/residue: 0.4624 time to fit residues: 157.0527 Evaluate side-chains 239 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 163 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 chunk 93 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 177 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 562 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.241976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.194021 restraints weight = 73845.676| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 3.50 r_work: 0.4395 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2338 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 22652 Z= 0.146 Angle : 0.743 20.456 31048 Z= 0.362 Chirality : 0.044 0.218 3601 Planarity : 0.005 0.049 3752 Dihedral : 12.468 84.776 3814 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.79 % Favored : 92.02 % Rotamer: Outliers : 3.73 % Allowed : 34.02 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.15), residues: 2650 helix: -0.52 (0.16), residues: 969 sheet: -1.43 (0.34), residues: 233 loop : -2.43 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 889 TYR 0.028 0.002 TYR A 831 PHE 0.022 0.002 PHE A 348 TRP 0.023 0.002 TRP A 598 HIS 0.007 0.001 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00313 (22620) covalent geometry : angle 0.72353 (31021) hydrogen bonds : bond 0.04915 ( 842) hydrogen bonds : angle 5.53618 ( 2324) metal coordination : bond 0.02409 ( 32) metal coordination : angle 5.73549 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 176 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2401 (OUTLIER) cc_final: 0.1020 (m170) REVERT: A 226 THR cc_start: 0.7835 (p) cc_final: 0.7590 (t) REVERT: A 242 MET cc_start: 0.2006 (OUTLIER) cc_final: 0.0555 (mtp) REVERT: A 566 MET cc_start: 0.2752 (mmt) cc_final: 0.1983 (mtt) REVERT: A 633 MET cc_start: 0.2032 (ttp) cc_final: -0.0196 (mpt) REVERT: A 666 MET cc_start: -0.0050 (OUTLIER) cc_final: -0.1331 (ptp) REVERT: A 882 HIS cc_start: 0.5448 (t-170) cc_final: 0.5216 (t70) REVERT: B 79 LYS cc_start: 0.1063 (pttt) cc_final: 0.0592 (mtmt) REVERT: B 94 MET cc_start: 0.1293 (ppp) cc_final: 0.0729 (tmm) REVERT: B 147 PHE cc_start: 0.3609 (p90) cc_final: 0.3164 (p90) REVERT: C 14 LEU cc_start: 0.0209 (OUTLIER) cc_final: -0.1656 (tp) REVERT: C 52 MET cc_start: 0.5371 (mmm) cc_final: 0.5093 (mmm) REVERT: D 70 MET cc_start: 0.1258 (ptm) cc_final: -0.0651 (mtt) REVERT: D 182 TRP cc_start: 0.0039 (OUTLIER) cc_final: -0.1242 (m100) REVERT: F 75 HIS cc_start: -0.0791 (OUTLIER) cc_final: -0.3248 (t-90) REVERT: F 93 TYR cc_start: -0.0226 (m-80) cc_final: -0.2087 (m-80) REVERT: F 122 LEU cc_start: 0.6319 (tt) cc_final: 0.5961 (mt) REVERT: F 131 LYS cc_start: -0.0748 (OUTLIER) cc_final: -0.1186 (tptt) REVERT: F 185 TYR cc_start: 0.7421 (p90) cc_final: 0.7012 (p90) REVERT: F 248 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4203 (tpm170) REVERT: F 289 SER cc_start: 0.1500 (OUTLIER) cc_final: 0.1244 (p) REVERT: F 391 LEU cc_start: 0.4168 (OUTLIER) cc_final: 0.3652 (mm) REVERT: F 526 LEU cc_start: -0.0086 (OUTLIER) cc_final: -0.0411 (pp) REVERT: F 551 GLU cc_start: -0.0028 (pt0) cc_final: -0.1804 (pm20) REVERT: E 32 ASP cc_start: 0.5148 (m-30) cc_final: 0.4257 (t70) REVERT: E 68 MET cc_start: 0.1130 (OUTLIER) cc_final: -0.0350 (pp-130) REVERT: E 73 LYS cc_start: 0.8360 (mppt) cc_final: 0.7893 (ttpp) REVERT: E 198 TYR cc_start: 0.4469 (OUTLIER) cc_final: 0.3942 (m-80) REVERT: E 233 MET cc_start: -0.2202 (mpm) cc_final: -0.3873 (tpt) REVERT: E 270 GLN cc_start: 0.7045 (tt0) cc_final: 0.6615 (mp10) REVERT: E 280 LEU cc_start: 0.3304 (mt) cc_final: 0.2555 (tp) REVERT: E 306 TYR cc_start: 0.3544 (m-80) cc_final: 0.3280 (m-80) REVERT: E 315 ASP cc_start: 0.4169 (OUTLIER) cc_final: 0.3944 (t0) REVERT: E 350 SER cc_start: 0.0789 (OUTLIER) cc_final: 0.0231 (m) REVERT: E 351 THR cc_start: 0.4587 (OUTLIER) cc_final: 0.4362 (t) REVERT: E 497 ARG cc_start: 0.4287 (OUTLIER) cc_final: 0.4004 (mmt90) REVERT: E 578 ASP cc_start: 0.1078 (OUTLIER) cc_final: 0.0696 (p0) REVERT: G 3 GLU cc_start: 0.1391 (OUTLIER) cc_final: -0.0491 (mm-30) REVERT: G 10 ARG cc_start: 0.2076 (OUTLIER) cc_final: 0.1240 (tpm170) REVERT: G 33 ASN cc_start: 0.5060 (t0) cc_final: 0.4784 (t0) outliers start: 84 outliers final: 41 residues processed: 246 average time/residue: 0.4125 time to fit residues: 122.6401 Evaluate side-chains 229 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 67 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 253 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 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 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN F 388 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.244559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.200712 restraints weight = 86534.590| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 4.48 r_work: 0.4450 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4434 r_free = 0.4434 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4434 r_free = 0.4434 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2463 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 22652 Z= 0.178 Angle : 0.815 22.439 31048 Z= 0.394 Chirality : 0.045 0.262 3601 Planarity : 0.005 0.066 3752 Dihedral : 12.564 83.635 3814 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.57 % Favored : 90.24 % Rotamer: Outliers : 4.21 % Allowed : 33.63 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.15), residues: 2650 helix: -0.63 (0.16), residues: 961 sheet: -1.37 (0.33), residues: 242 loop : -2.47 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 560 TYR 0.030 0.002 TYR A 595 PHE 0.033 0.003 PHE A 843 TRP 0.021 0.002 TRP A 800 HIS 0.010 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00383 (22620) covalent geometry : angle 0.78825 (31021) hydrogen bonds : bond 0.05388 ( 842) hydrogen bonds : angle 5.73958 ( 2324) metal coordination : bond 0.02566 ( 32) metal coordination : angle 7.10230 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 181 time to evaluate : 0.899 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 113 HIS cc_start: 0.2398 (OUTLIER) cc_final: 0.1042 (m170) REVERT: A 242 MET cc_start: 0.2146 (OUTLIER) cc_final: 0.0939 (mtt) REVERT: A 411 LYS cc_start: 0.1981 (mtmt) cc_final: 0.1563 (mmmt) REVERT: A 566 MET cc_start: 0.2628 (mmt) cc_final: 0.1935 (mtt) REVERT: A 633 MET cc_start: 0.2142 (ttp) cc_final: -0.0236 (mpm) REVERT: A 666 MET cc_start: 0.0246 (OUTLIER) cc_final: -0.1102 (ptp) REVERT: A 770 TYR cc_start: -0.0727 (OUTLIER) cc_final: -0.2059 (m-10) REVERT: A 924 MET cc_start: 0.2856 (tpt) cc_final: 0.2411 (tpt) REVERT: B 79 LYS cc_start: 0.1195 (pttt) cc_final: 0.0606 (mtmt) REVERT: B 94 MET cc_start: 0.1110 (ppp) cc_final: 0.0809 (tmm) REVERT: B 147 PHE cc_start: 0.3720 (p90) cc_final: 0.3194 (p90) REVERT: C 14 LEU cc_start: 0.0598 (OUTLIER) cc_final: -0.1219 (tp) REVERT: D 55 MET cc_start: 0.2431 (mmm) cc_final: 0.1536 (ptp) REVERT: D 67 MET cc_start: -0.1171 (ttt) cc_final: -0.1589 (ptt) REVERT: D 70 MET cc_start: 0.1398 (ptm) cc_final: -0.0665 (mtt) REVERT: D 87 MET cc_start: 0.1412 (mpt) cc_final: 0.0738 (mpt) REVERT: D 127 LYS cc_start: 0.4933 (ttpp) cc_final: 0.4715 (tptp) REVERT: F 75 HIS cc_start: -0.0532 (OUTLIER) cc_final: -0.3019 (t-90) REVERT: F 93 TYR cc_start: -0.0301 (m-80) cc_final: -0.2257 (m-80) REVERT: F 122 LEU cc_start: 0.6245 (tt) cc_final: 0.5898 (mt) REVERT: F 131 LYS cc_start: -0.0719 (OUTLIER) cc_final: -0.1253 (tptt) REVERT: F 185 TYR cc_start: 0.7367 (p90) cc_final: 0.6906 (p90) REVERT: F 248 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.3931 (tpm170) REVERT: F 289 SER cc_start: 0.1239 (OUTLIER) cc_final: 0.0990 (p) REVERT: F 391 LEU cc_start: 0.3726 (OUTLIER) cc_final: 0.3269 (mm) REVERT: F 526 LEU cc_start: -0.0427 (OUTLIER) cc_final: -0.0770 (pp) REVERT: E 32 ASP cc_start: 0.4938 (m-30) cc_final: 0.4269 (t70) REVERT: E 198 TYR cc_start: 0.4529 (OUTLIER) cc_final: 0.4045 (m-80) REVERT: E 233 MET cc_start: -0.1782 (mpm) cc_final: -0.3658 (tpt) REVERT: E 270 GLN cc_start: 0.7077 (tt0) cc_final: 0.6649 (mp10) REVERT: E 280 LEU cc_start: 0.3389 (mt) cc_final: 0.2681 (tm) REVERT: E 306 TYR cc_start: 0.3848 (m-80) cc_final: 0.3409 (m-80) REVERT: E 315 ASP cc_start: 0.4018 (OUTLIER) cc_final: 0.3765 (t0) REVERT: E 350 SER cc_start: 0.0432 (OUTLIER) cc_final: -0.0155 (m) REVERT: E 351 THR cc_start: 0.4548 (OUTLIER) cc_final: 0.4304 (t) REVERT: E 497 ARG cc_start: 0.4060 (OUTLIER) cc_final: 0.3797 (mmt90) REVERT: E 578 ASP cc_start: 0.0842 (OUTLIER) cc_final: 0.0484 (p0) REVERT: G 3 GLU cc_start: 0.1042 (OUTLIER) cc_final: -0.0768 (mm-30) REVERT: G 10 ARG cc_start: 0.1937 (OUTLIER) cc_final: 0.1136 (tpm170) REVERT: G 33 ASN cc_start: 0.4949 (t0) cc_final: 0.4688 (t0) REVERT: G 74 ARG cc_start: 0.4990 (ttm-80) cc_final: 0.4166 (ttp80) outliers start: 95 outliers final: 58 residues processed: 256 average time/residue: 0.4806 time to fit residues: 147.2335 Evaluate side-chains 250 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 173 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 816 HIS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 133 optimal weight: 3.9990 chunk 32 optimal weight: 0.0050 chunk 255 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 249 optimal weight: 0.4980 chunk 226 optimal weight: 20.0000 chunk 87 optimal weight: 0.0050 chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 0.0000 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS A 886 GLN A 892 HIS B 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS E 46 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.244592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.200566 restraints weight = 85112.974| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 4.81 r_work: 0.4426 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4405 r_free = 0.4405 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4405 r_free = 0.4405 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2254 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22652 Z= 0.126 Angle : 0.727 16.525 31048 Z= 0.346 Chirality : 0.043 0.290 3601 Planarity : 0.005 0.050 3752 Dihedral : 12.287 81.648 3813 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.11 % Favored : 92.70 % Rotamer: Outliers : 3.03 % Allowed : 34.99 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.16), residues: 2650 helix: -0.31 (0.17), residues: 969 sheet: -1.17 (0.35), residues: 230 loop : -2.32 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 560 TYR 0.020 0.001 TYR E 277 PHE 0.018 0.001 PHE A 102 TRP 0.022 0.002 TRP A 598 HIS 0.014 0.001 HIS E 554 Details of bonding type rmsd covalent geometry : bond 0.00268 (22620) covalent geometry : angle 0.70290 (31021) hydrogen bonds : bond 0.04483 ( 842) hydrogen bonds : angle 5.22651 ( 2324) metal coordination : bond 0.02218 ( 32) metal coordination : angle 6.35572 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 173 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2286 (OUTLIER) cc_final: 0.0844 (m170) REVERT: A 196 MET cc_start: 0.3523 (mmm) cc_final: 0.1963 (mtm) REVERT: A 226 THR cc_start: 0.7741 (p) cc_final: 0.7485 (t) REVERT: A 235 ASP cc_start: 0.2695 (OUTLIER) cc_final: 0.2432 (t70) REVERT: A 239 SER cc_start: 0.1631 (OUTLIER) cc_final: 0.1186 (t) REVERT: A 242 MET cc_start: 0.1829 (OUTLIER) cc_final: 0.1441 (mtt) REVERT: A 405 VAL cc_start: 0.0659 (OUTLIER) cc_final: 0.0423 (m) REVERT: A 411 LYS cc_start: 0.1741 (mtmt) cc_final: 0.1460 (mmmt) REVERT: A 566 MET cc_start: 0.2721 (mmt) cc_final: 0.2237 (mtt) REVERT: A 633 MET cc_start: 0.1957 (ttp) cc_final: -0.0267 (mpm) REVERT: A 666 MET cc_start: 0.0010 (OUTLIER) cc_final: -0.1261 (ptp) REVERT: A 835 SER cc_start: 0.7477 (t) cc_final: 0.7219 (m) REVERT: A 924 MET cc_start: 0.2440 (tpt) cc_final: 0.2081 (tpt) REVERT: B 79 LYS cc_start: 0.1109 (pttt) cc_final: 0.0757 (mtmt) REVERT: B 147 PHE cc_start: 0.3449 (p90) cc_final: 0.3064 (p90) REVERT: D 55 MET cc_start: 0.2621 (mmm) cc_final: 0.1732 (ptm) REVERT: D 67 MET cc_start: -0.1371 (ttt) cc_final: -0.1827 (ptt) REVERT: D 70 MET cc_start: 0.0907 (ptm) cc_final: -0.0747 (mtt) REVERT: D 87 MET cc_start: 0.1291 (mpt) cc_final: 0.0802 (mpt) REVERT: F 75 HIS cc_start: -0.0523 (OUTLIER) cc_final: -0.3019 (t-90) REVERT: F 93 TYR cc_start: -0.0410 (m-80) cc_final: -0.2336 (m-80) REVERT: F 122 LEU cc_start: 0.6265 (tt) cc_final: 0.5895 (mt) REVERT: F 131 LYS cc_start: -0.0700 (OUTLIER) cc_final: -0.1221 (tptt) REVERT: F 185 TYR cc_start: 0.7306 (p90) cc_final: 0.6866 (p90) REVERT: F 248 ARG cc_start: 0.4892 (OUTLIER) cc_final: 0.3868 (tpm170) REVERT: F 274 MET cc_start: 0.7033 (ptm) cc_final: 0.6484 (ppp) REVERT: F 289 SER cc_start: 0.1236 (OUTLIER) cc_final: 0.0990 (p) REVERT: F 391 LEU cc_start: 0.3639 (OUTLIER) cc_final: 0.3198 (mm) REVERT: F 526 LEU cc_start: -0.0419 (OUTLIER) cc_final: -0.0744 (pp) REVERT: E 32 ASP cc_start: 0.4971 (m-30) cc_final: 0.4210 (t70) REVERT: E 73 LYS cc_start: 0.8457 (mppt) cc_final: 0.7934 (ttpp) REVERT: E 233 MET cc_start: -0.1657 (mpm) cc_final: -0.3526 (tpt) REVERT: E 270 GLN cc_start: 0.7074 (tt0) cc_final: 0.6680 (mp10) REVERT: E 280 LEU cc_start: 0.3373 (mt) cc_final: 0.2644 (tm) REVERT: E 306 TYR cc_start: 0.3717 (m-80) cc_final: 0.3421 (m-80) REVERT: E 315 ASP cc_start: 0.3942 (OUTLIER) cc_final: 0.3701 (t0) REVERT: E 350 SER cc_start: 0.0284 (OUTLIER) cc_final: -0.0280 (m) REVERT: E 351 THR cc_start: 0.4493 (OUTLIER) cc_final: 0.4242 (t) REVERT: E 453 SER cc_start: 0.2669 (m) cc_final: 0.2389 (p) REVERT: E 497 ARG cc_start: 0.4197 (OUTLIER) cc_final: 0.3907 (mmt90) REVERT: E 578 ASP cc_start: 0.0926 (OUTLIER) cc_final: 0.0540 (p0) REVERT: G 3 GLU cc_start: 0.1169 (OUTLIER) cc_final: -0.0399 (mm-30) REVERT: G 10 ARG cc_start: 0.2012 (OUTLIER) cc_final: 0.1062 (tpm170) REVERT: G 32 TYR cc_start: 0.1203 (m-80) cc_final: -0.0392 (m-80) REVERT: G 33 ASN cc_start: 0.5072 (t0) cc_final: 0.4865 (t0) REVERT: G 87 TYR cc_start: 0.3722 (m-80) cc_final: 0.3409 (m-80) REVERT: G 101 MET cc_start: 0.5292 (pp-130) cc_final: 0.3954 (mmp) outliers start: 68 outliers final: 37 residues processed: 225 average time/residue: 0.4916 time to fit residues: 131.9692 Evaluate side-chains 224 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 30.0000 chunk 176 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 108 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN ** E 548 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 = 0.5044 r_free = 0.5044 target = 0.245668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.202909 restraints weight = 76392.147| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 4.67 r_work: 0.4458 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2376 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22652 Z= 0.147 Angle : 0.747 16.394 31048 Z= 0.358 Chirality : 0.043 0.287 3601 Planarity : 0.005 0.057 3752 Dihedral : 12.327 80.973 3813 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.70 % Favored : 91.15 % Rotamer: Outliers : 2.85 % Allowed : 35.21 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.16), residues: 2650 helix: -0.31 (0.17), residues: 970 sheet: -1.22 (0.36), residues: 214 loop : -2.30 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 560 TYR 0.022 0.002 TYR A 788 PHE 0.024 0.002 PHE A 843 TRP 0.015 0.002 TRP A 598 HIS 0.006 0.001 HIS A 816 Details of bonding type rmsd covalent geometry : bond 0.00316 (22620) covalent geometry : angle 0.72563 (31021) hydrogen bonds : bond 0.04699 ( 842) hydrogen bonds : angle 5.33520 ( 2324) metal coordination : bond 0.02534 ( 32) metal coordination : angle 6.11432 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2418 (OUTLIER) cc_final: 0.1048 (m170) REVERT: A 242 MET cc_start: 0.2098 (OUTLIER) cc_final: 0.1597 (mtt) REVERT: A 411 LYS cc_start: 0.1889 (mtmt) cc_final: 0.1497 (mmmt) REVERT: A 566 MET cc_start: 0.2774 (mmt) cc_final: 0.2156 (mtt) REVERT: A 633 MET cc_start: 0.2251 (ttp) cc_final: -0.0413 (mpm) REVERT: A 666 MET cc_start: 0.0162 (OUTLIER) cc_final: -0.1047 (ptp) REVERT: A 835 SER cc_start: 0.7624 (t) cc_final: 0.7397 (m) REVERT: A 924 MET cc_start: 0.2652 (tpt) cc_final: 0.2013 (tpt) REVERT: B 147 PHE cc_start: 0.3412 (p90) cc_final: 0.2877 (p90) REVERT: B 176 ASN cc_start: 0.5929 (t0) cc_final: 0.5068 (m-40) REVERT: C 14 LEU cc_start: 0.0253 (OUTLIER) cc_final: -0.1626 (tp) REVERT: D 55 MET cc_start: 0.2723 (mmm) cc_final: 0.1746 (ptm) REVERT: D 70 MET cc_start: 0.1078 (ptm) cc_final: -0.0638 (mtt) REVERT: D 87 MET cc_start: 0.1601 (mpt) cc_final: 0.1039 (mpt) REVERT: F 75 HIS cc_start: -0.0658 (OUTLIER) cc_final: -0.3221 (t-90) REVERT: F 93 TYR cc_start: -0.0416 (m-80) cc_final: -0.2365 (m-80) REVERT: F 122 LEU cc_start: 0.6188 (tt) cc_final: 0.5832 (mt) REVERT: F 131 LYS cc_start: -0.0729 (OUTLIER) cc_final: -0.1250 (tptt) REVERT: F 185 TYR cc_start: 0.7286 (p90) cc_final: 0.6833 (p90) REVERT: F 248 ARG cc_start: 0.4672 (OUTLIER) cc_final: 0.3731 (tpm170) REVERT: F 253 TYR cc_start: 0.3733 (OUTLIER) cc_final: 0.3323 (t80) REVERT: F 274 MET cc_start: 0.7124 (ptm) cc_final: 0.6788 (ppp) REVERT: F 289 SER cc_start: 0.1234 (OUTLIER) cc_final: 0.0984 (p) REVERT: F 391 LEU cc_start: 0.3624 (OUTLIER) cc_final: 0.3190 (mm) REVERT: F 526 LEU cc_start: -0.0558 (OUTLIER) cc_final: -0.0894 (pp) REVERT: E 32 ASP cc_start: 0.4915 (m-30) cc_final: 0.4164 (t70) REVERT: E 73 LYS cc_start: 0.8485 (mppt) cc_final: 0.7984 (ttpp) REVERT: E 122 LEU cc_start: 0.5284 (pp) cc_final: 0.5053 (pt) REVERT: E 233 MET cc_start: -0.1590 (mpm) cc_final: -0.3521 (tpt) REVERT: E 270 GLN cc_start: 0.7041 (tt0) cc_final: 0.6624 (mp10) REVERT: E 280 LEU cc_start: 0.3418 (mt) cc_final: 0.2684 (tm) REVERT: E 306 TYR cc_start: 0.3761 (m-80) cc_final: 0.3395 (m-80) REVERT: E 315 ASP cc_start: 0.3677 (OUTLIER) cc_final: 0.3450 (t0) REVERT: E 350 SER cc_start: 0.0277 (OUTLIER) cc_final: -0.0279 (m) REVERT: E 351 THR cc_start: 0.4600 (OUTLIER) cc_final: 0.4348 (t) REVERT: E 497 ARG cc_start: 0.4190 (OUTLIER) cc_final: 0.3903 (mmt90) REVERT: E 578 ASP cc_start: 0.0838 (OUTLIER) cc_final: 0.0628 (p0) REVERT: G 3 GLU cc_start: 0.1160 (OUTLIER) cc_final: -0.0555 (mm-30) REVERT: G 10 ARG cc_start: 0.2051 (OUTLIER) cc_final: 0.1341 (tpm170) REVERT: G 33 ASN cc_start: 0.5128 (t0) cc_final: 0.4858 (t0) REVERT: G 74 ARG cc_start: 0.5087 (ttm-80) cc_final: 0.4646 (tmt-80) REVERT: G 101 MET cc_start: 0.5271 (pp-130) cc_final: 0.3749 (mmm) outliers start: 64 outliers final: 40 residues processed: 214 average time/residue: 0.5218 time to fit residues: 133.0019 Evaluate side-chains 219 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 881 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 89 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 0.0070 chunk 92 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 200 optimal weight: 0.0070 chunk 121 optimal weight: 0.7980 chunk 160 optimal weight: 0.0030 chunk 82 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 108 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.245516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.201646 restraints weight = 87528.604| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 4.97 r_work: 0.4453 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2217 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22652 Z= 0.122 Angle : 0.699 15.972 31048 Z= 0.331 Chirality : 0.042 0.289 3601 Planarity : 0.004 0.056 3752 Dihedral : 12.160 79.238 3813 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.30 % Favored : 92.55 % Rotamer: Outliers : 2.63 % Allowed : 35.43 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.16), residues: 2650 helix: -0.10 (0.17), residues: 976 sheet: -1.06 (0.34), residues: 248 loop : -2.18 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 560 TYR 0.020 0.001 TYR G 89 PHE 0.016 0.001 PHE A 741 TRP 0.020 0.002 TRP A 216 HIS 0.005 0.001 HIS A 642 Details of bonding type rmsd covalent geometry : bond 0.00255 (22620) covalent geometry : angle 0.67762 (31021) hydrogen bonds : bond 0.04267 ( 842) hydrogen bonds : angle 5.02966 ( 2324) metal coordination : bond 0.02072 ( 32) metal coordination : angle 5.80816 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12626.18 seconds wall clock time: 215 minutes 10.50 seconds (12910.50 seconds total)