Starting phenix.real_space_refine on Thu Jun 19 12:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwe_34310/06_2025/8gwe_34310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwe_34310/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwe_34310/06_2025/8gwe_34310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwe_34310/06_2025/8gwe_34310.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwe_34310/06_2025/8gwe_34310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwe_34310/06_2025/8gwe_34310.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 1, 'GLN: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: 17.55, per 1000 atoms: 0.80 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: 6.20 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 7.35 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: 7.77 Time building geometry restraints manager: 7.17 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 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 593 or resid 701 throug \ h 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: 5.590 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: 0.010 Extract box with map and model: 1.130 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 65.570 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (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 TRP 0.038 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 PHE 0.017 0.001 PHE F 437 TYR 0.021 0.001 TYR F 299 ARG 0.006 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.18410 ( 842) hydrogen bonds : angle 6.40337 ( 2324) metal coordination : bond 0.01929 ( 32) metal coordination : angle 5.21557 ( 27) covalent geometry : bond 0.00879 (22620) covalent geometry : angle 0.97279 (31021) *********************** 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 : 2.477 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: 0.9211 time to fit residues: 422.3812 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 : 2.358 ------------------------------------------------------------------------------- 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 225 optimal weight: 20.0000 chunk 202 optimal weight: 0.0070 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 chunk 209 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 242 optimal weight: 7.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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 439 HIS A 492 GLN A 534 ASN A 790 ASN A 911 ASN C 19 GLN D 176 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 98 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.222847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.157607 restraints weight = 61330.618| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 4.27 r_work: 0.3951 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1348 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 22652 Z= 0.182 Angle : 0.795 15.676 31048 Z= 0.395 Chirality : 0.046 0.432 3601 Planarity : 0.005 0.064 3752 Dihedral : 12.959 83.317 3843 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.81 % Favored : 90.92 % Rotamer: Outliers : 5.40 % Allowed : 32.22 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2650 helix: 0.25 (0.17), residues: 948 sheet: -1.29 (0.33), residues: 233 loop : -2.42 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 182 HIS 0.010 0.001 HIS A 752 PHE 0.024 0.002 PHE F 90 TYR 0.028 0.002 TYR A 129 ARG 0.008 0.001 ARG F 497 Details of bonding type rmsd hydrogen bonds : bond 0.05562 ( 842) hydrogen bonds : angle 5.41642 ( 2324) metal coordination : bond 0.02333 ( 32) metal coordination : angle 5.89200 ( 27) covalent geometry : bond 0.00397 (22620) covalent geometry : angle 0.77591 (31021) *********************** 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 306 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 184 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.1242 (OUTLIER) cc_final: 0.0659 (pttt) REVERT: A 162 TRP cc_start: 0.1360 (p-90) cc_final: -0.0241 (p-90) REVERT: A 226 THR cc_start: 0.7491 (p) cc_final: 0.7163 (t) REVERT: A 235 ASP cc_start: 0.2861 (OUTLIER) cc_final: 0.2087 (m-30) REVERT: A 566 MET cc_start: 0.3600 (ttm) cc_final: 0.3017 (mmt) REVERT: A 633 MET cc_start: 0.0770 (ttp) cc_final: -0.1418 (mpp) REVERT: A 648 LEU cc_start: -0.0692 (OUTLIER) cc_final: -0.1308 (mm) REVERT: A 666 MET cc_start: 0.0002 (OUTLIER) cc_final: -0.0788 (pmm) REVERT: A 925 TYR cc_start: 0.2703 (m-80) cc_final: 0.2284 (m-80) REVERT: B 51 ARG cc_start: 0.2073 (mpp-170) cc_final: 0.1584 (tpp80) REVERT: D 42 LEU cc_start: 0.0423 (OUTLIER) cc_final: 0.0106 (mt) REVERT: D 70 MET cc_start: 0.0835 (ptm) cc_final: -0.0027 (mtp) REVERT: D 139 LYS cc_start: 0.7204 (ttpp) cc_final: 0.6780 (tppt) REVERT: D 140 ASN cc_start: 0.6497 (m-40) cc_final: 0.6009 (t0) REVERT: D 182 TRP cc_start: -0.0842 (OUTLIER) cc_final: -0.1799 (m100) REVERT: F 122 LEU cc_start: 0.6134 (tt) cc_final: 0.5645 (mt) REVERT: F 128 GLU cc_start: 0.3021 (tp30) cc_final: 0.2768 (mm-30) REVERT: F 185 TYR cc_start: 0.7149 (p90) cc_final: 0.6672 (p90) REVERT: F 493 ILE cc_start: -0.0112 (OUTLIER) cc_final: -0.0409 (tp) REVERT: E 68 MET cc_start: 0.0480 (OUTLIER) cc_final: -0.1188 (pp-130) REVERT: E 233 MET cc_start: -0.2922 (OUTLIER) cc_final: -0.4470 (tpt) REVERT: E 270 GLN cc_start: 0.7120 (tt0) cc_final: 0.6428 (mp10) REVERT: E 280 LEU cc_start: 0.3674 (mt) cc_final: 0.3282 (tm) REVERT: E 315 ASP cc_start: 0.4387 (OUTLIER) cc_final: 0.3962 (t0) REVERT: E 579 ARG cc_start: 0.4088 (tpp-160) cc_final: 0.3807 (tpp-160) REVERT: G 10 ARG cc_start: 0.2696 (OUTLIER) cc_final: 0.2125 (tpt90) REVERT: G 33 ASN cc_start: 0.5599 (t0) cc_final: 0.5298 (t0) REVERT: G 73 CYS cc_start: 0.5360 (t) cc_final: 0.4537 (m) REVERT: G 88 LEU cc_start: 0.3917 (OUTLIER) cc_final: 0.2471 (pp) REVERT: G 89 TYR cc_start: 0.0681 (m-80) cc_final: 0.0273 (m-10) outliers start: 122 outliers final: 34 residues processed: 284 average time/residue: 1.1025 time to fit residues: 366.7242 Evaluate side-chains 202 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 59 LYS 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 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 648 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 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 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 351 THR 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 E residue 12 THR Chi-restraints excluded: chain E residue 68 MET 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 88 LEU 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 83 optimal weight: 0.1980 chunk 207 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 195 optimal weight: 0.1980 chunk 261 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 464 HIS F 516 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.226115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.162087 restraints weight = 64267.366| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 4.36 r_work: 0.4005 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1482 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22652 Z= 0.147 Angle : 0.717 15.976 31048 Z= 0.358 Chirality : 0.044 0.235 3601 Planarity : 0.005 0.059 3752 Dihedral : 12.630 82.955 3822 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.83 % Favored : 91.91 % Rotamer: Outliers : 4.74 % Allowed : 32.18 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2650 helix: 0.14 (0.17), residues: 956 sheet: -0.96 (0.35), residues: 227 loop : -2.40 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 182 HIS 0.007 0.001 HIS A 309 PHE 0.018 0.002 PHE E 422 TYR 0.040 0.002 TYR E 299 ARG 0.007 0.001 ARG F 427 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 842) hydrogen bonds : angle 5.14848 ( 2324) metal coordination : bond 0.02789 ( 32) metal coordination : angle 5.54165 ( 27) covalent geometry : bond 0.00311 (22620) covalent geometry : angle 0.69829 (31021) *********************** 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 281 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 174 time to evaluate : 2.374 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 162 TRP cc_start: 0.1246 (p-90) cc_final: -0.0421 (p-90) REVERT: A 226 THR cc_start: 0.7447 (p) cc_final: 0.7083 (t) REVERT: A 235 ASP cc_start: 0.2727 (OUTLIER) cc_final: 0.2457 (t70) REVERT: A 633 MET cc_start: 0.0603 (ttp) cc_final: -0.1524 (mpp) REVERT: A 666 MET cc_start: 0.0210 (OUTLIER) cc_final: -0.0421 (pmm) REVERT: A 886 GLN cc_start: 0.5242 (mt0) cc_final: 0.4839 (mt0) REVERT: A 925 TYR cc_start: 0.2961 (m-80) cc_final: 0.2313 (m-80) REVERT: D 42 LEU cc_start: 0.0343 (OUTLIER) cc_final: 0.0033 (mt) REVERT: D 70 MET cc_start: 0.0731 (ptm) cc_final: -0.0491 (mtp) REVERT: D 129 MET cc_start: 0.2568 (ptp) cc_final: 0.0648 (tpp) REVERT: D 139 LYS cc_start: 0.7162 (ttpp) cc_final: 0.6768 (tppt) REVERT: D 140 ASN cc_start: 0.6503 (m-40) cc_final: 0.5936 (t0) REVERT: D 182 TRP cc_start: -0.0620 (OUTLIER) cc_final: -0.1605 (m100) REVERT: F 122 LEU cc_start: 0.6201 (tt) cc_final: 0.5692 (mt) REVERT: F 185 TYR cc_start: 0.7237 (p90) cc_final: 0.6696 (p90) REVERT: F 289 SER cc_start: 0.1224 (OUTLIER) cc_final: 0.0919 (p) REVERT: F 493 ILE cc_start: -0.0027 (OUTLIER) cc_final: -0.0333 (tp) REVERT: E 68 MET cc_start: 0.0430 (OUTLIER) cc_final: -0.1146 (pp-130) REVERT: E 73 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7738 (ttpp) REVERT: E 155 ARG cc_start: 0.1596 (mmt180) cc_final: 0.0681 (tpp80) REVERT: E 198 TYR cc_start: 0.4168 (OUTLIER) cc_final: 0.3764 (m-80) REVERT: E 199 THR cc_start: 0.4133 (OUTLIER) cc_final: 0.3509 (t) REVERT: E 233 MET cc_start: -0.2786 (mpm) cc_final: -0.4276 (tpt) REVERT: E 270 GLN cc_start: 0.7182 (tt0) cc_final: 0.6501 (mp10) REVERT: E 280 LEU cc_start: 0.4045 (mt) cc_final: 0.3659 (tm) REVERT: E 315 ASP cc_start: 0.4346 (OUTLIER) cc_final: 0.3900 (t0) REVERT: E 582 TYR cc_start: 0.3483 (t80) cc_final: 0.3110 (t80) REVERT: G 10 ARG cc_start: 0.2625 (OUTLIER) cc_final: 0.1814 (tpp-160) REVERT: G 47 ASP cc_start: 0.0132 (OUTLIER) cc_final: -0.0103 (t0) REVERT: G 88 LEU cc_start: 0.3731 (OUTLIER) cc_final: 0.2416 (tm) outliers start: 107 outliers final: 44 residues processed: 261 average time/residue: 0.9597 time to fit residues: 302.0110 Evaluate side-chains 214 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP 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 329 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 588 VAL 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 776 VAL 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 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 59 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 81 PHE Chi-restraints excluded: chain F residue 120 TYR 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 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 68 MET Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 315 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 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 63 optimal weight: 0.5980 chunk 232 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 185 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 447 ASN A 572 HIS A 611 ASN A 650 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 725 HIS A 875 GLN ** 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 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.231717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.173376 restraints weight = 84295.045| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 5.02 r_work: 0.4070 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1896 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22652 Z= 0.178 Angle : 0.763 14.421 31048 Z= 0.385 Chirality : 0.046 0.320 3601 Planarity : 0.005 0.052 3752 Dihedral : 12.669 84.550 3822 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.81 % Favored : 90.92 % Rotamer: Outliers : 5.79 % Allowed : 31.26 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2650 helix: -0.24 (0.17), residues: 961 sheet: -0.98 (0.36), residues: 218 loop : -2.34 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 182 HIS 0.013 0.002 HIS A 309 PHE 0.032 0.002 PHE A 348 TYR 0.053 0.002 TYR F 476 ARG 0.006 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.05151 ( 842) hydrogen bonds : angle 5.36506 ( 2324) metal coordination : bond 0.02142 ( 32) metal coordination : angle 4.47864 ( 27) covalent geometry : bond 0.00377 (22620) covalent geometry : angle 0.75224 (31021) *********************** 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 311 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 180 time to evaluate : 2.400 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 226 THR cc_start: 0.7908 (p) cc_final: 0.7475 (t) REVERT: A 242 MET cc_start: 0.1953 (OUTLIER) cc_final: 0.1321 (mtp) REVERT: A 477 ASP cc_start: -0.1311 (OUTLIER) cc_final: -0.1618 (m-30) REVERT: A 633 MET cc_start: 0.1701 (ttp) cc_final: -0.0737 (mpp) REVERT: A 666 MET cc_start: 0.0312 (OUTLIER) cc_final: -0.0475 (pmm) REVERT: A 778 SER cc_start: -0.1864 (OUTLIER) cc_final: -0.2118 (t) REVERT: A 886 GLN cc_start: 0.5231 (mt0) cc_final: 0.4998 (mt0) REVERT: B 79 LYS cc_start: -0.0206 (pptt) cc_final: -0.1303 (mtmt) REVERT: C 68 ILE cc_start: -0.2944 (OUTLIER) cc_final: -0.3298 (mm) REVERT: D 42 LEU cc_start: 0.0187 (OUTLIER) cc_final: -0.0203 (mt) REVERT: D 70 MET cc_start: 0.0946 (ptm) cc_final: -0.0535 (mtt) REVERT: D 139 LYS cc_start: 0.7140 (ttpp) cc_final: 0.6750 (tppt) REVERT: D 140 ASN cc_start: 0.6472 (m-40) cc_final: 0.5896 (t0) REVERT: D 182 TRP cc_start: -0.0490 (OUTLIER) cc_final: -0.1505 (m100) REVERT: F 122 LEU cc_start: 0.6291 (tt) cc_final: 0.5790 (mt) REVERT: F 185 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6710 (p90) REVERT: F 248 ARG cc_start: 0.4690 (OUTLIER) cc_final: 0.3966 (tpm170) REVERT: F 289 SER cc_start: 0.1376 (OUTLIER) cc_final: 0.1066 (p) REVERT: F 526 LEU cc_start: -0.0165 (OUTLIER) cc_final: -0.0508 (pp) REVERT: E 73 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7714 (ttpp) REVERT: E 155 ARG cc_start: 0.1446 (mmt180) cc_final: 0.0545 (tpp80) REVERT: E 198 TYR cc_start: 0.4343 (OUTLIER) cc_final: 0.3846 (m-80) REVERT: E 199 THR cc_start: 0.4305 (OUTLIER) cc_final: 0.3593 (t) REVERT: E 233 MET cc_start: -0.2825 (OUTLIER) cc_final: -0.4507 (tpt) REVERT: E 270 GLN cc_start: 0.7190 (tt0) cc_final: 0.6604 (mp10) REVERT: E 280 LEU cc_start: 0.3293 (OUTLIER) cc_final: 0.2758 (tp) REVERT: E 315 ASP cc_start: 0.4481 (OUTLIER) cc_final: 0.4108 (t0) REVERT: E 350 SER cc_start: -0.0292 (OUTLIER) cc_final: -0.1012 (m) REVERT: G 3 GLU cc_start: 0.1047 (OUTLIER) cc_final: -0.0374 (mm-30) REVERT: G 10 ARG cc_start: 0.2486 (OUTLIER) cc_final: 0.1329 (tpm170) REVERT: G 47 ASP cc_start: 0.0291 (OUTLIER) cc_final: 0.0075 (t0) outliers start: 131 outliers final: 51 residues processed: 284 average time/residue: 1.4380 time to fit residues: 489.5779 Evaluate side-chains 233 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 161 time to evaluate : 3.200 ------------------------------------------------------------------------------- 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 242 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 ASP 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 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 742 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 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 6 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 59 LEU 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 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 25 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ILE 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 253 TYR 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 495 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 555 SER 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 73 LYS Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 280 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 578 ASP Chi-restraints excluded: chain E residue 588 THR 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 47 ASP Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 60 optimal weight: 0.7980 chunk 163 optimal weight: 0.0010 chunk 42 optimal weight: 0.4980 chunk 207 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 137 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN A 703 ASN A 874 ASN ** A 882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.232865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.174761 restraints weight = 74436.283| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 4.63 r_work: 0.4117 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1848 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 22652 Z= 0.127 Angle : 0.673 14.827 31048 Z= 0.333 Chirality : 0.042 0.244 3601 Planarity : 0.004 0.055 3752 Dihedral : 12.393 82.432 3819 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.94 % Favored : 91.83 % Rotamer: Outliers : 4.35 % Allowed : 33.23 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2650 helix: 0.02 (0.17), residues: 964 sheet: -0.84 (0.37), residues: 220 loop : -2.24 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 598 HIS 0.012 0.001 HIS A 642 PHE 0.033 0.002 PHE A 471 TYR 0.023 0.002 TYR E 382 ARG 0.005 0.001 ARG F 427 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 842) hydrogen bonds : angle 5.00896 ( 2324) metal coordination : bond 0.02367 ( 32) metal coordination : angle 4.63825 ( 27) covalent geometry : bond 0.00267 (22620) covalent geometry : angle 0.65919 (31021) *********************** 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 266 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 168 time to evaluate : 2.359 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: 0.1873 (OUTLIER) cc_final: 0.0154 (m170) REVERT: A 226 THR cc_start: 0.7813 (p) cc_final: 0.7395 (t) REVERT: A 239 SER cc_start: 0.1009 (OUTLIER) cc_final: 0.0546 (t) REVERT: A 633 MET cc_start: 0.1908 (ttp) cc_final: -0.0650 (mpp) REVERT: A 666 MET cc_start: 0.0343 (OUTLIER) cc_final: -0.0096 (pmm) REVERT: B 79 LYS cc_start: 0.0651 (pptt) cc_final: -0.0918 (mtmt) REVERT: D 42 LEU cc_start: -0.0014 (OUTLIER) cc_final: -0.0465 (mt) REVERT: D 70 MET cc_start: 0.0768 (ptm) cc_final: -0.0547 (mtt) REVERT: D 139 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6806 (tppt) REVERT: D 140 ASN cc_start: 0.6441 (m-40) cc_final: 0.5719 (t0) REVERT: D 182 TRP cc_start: -0.0166 (OUTLIER) cc_final: -0.1329 (m100) REVERT: F 75 HIS cc_start: -0.0402 (OUTLIER) cc_final: -0.2600 (t-90) REVERT: F 122 LEU cc_start: 0.6230 (tt) cc_final: 0.5763 (mt) REVERT: F 131 LYS cc_start: -0.0831 (OUTLIER) cc_final: -0.1297 (tptt) REVERT: F 176 LEU cc_start: 0.2341 (tm) cc_final: 0.2101 (tp) REVERT: F 185 TYR cc_start: 0.7242 (p90) cc_final: 0.6757 (p90) REVERT: F 248 ARG cc_start: 0.4887 (OUTLIER) cc_final: 0.4012 (tpm170) REVERT: F 254 PRO cc_start: 0.4434 (Cg_exo) cc_final: 0.4055 (Cg_endo) REVERT: F 289 SER cc_start: 0.1105 (OUTLIER) cc_final: 0.0834 (p) REVERT: F 526 LEU cc_start: -0.0344 (OUTLIER) cc_final: -0.0688 (pp) REVERT: E 12 THR cc_start: -0.1159 (OUTLIER) cc_final: -0.1400 (t) REVERT: E 21 ARG cc_start: -0.1763 (OUTLIER) cc_final: -0.2524 (ppp80) REVERT: E 68 MET cc_start: 0.0197 (OUTLIER) cc_final: -0.1107 (pp-130) REVERT: E 73 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7949 (ttpp) REVERT: E 155 ARG cc_start: 0.1297 (mmt180) cc_final: 0.0628 (tpp80) REVERT: E 198 TYR cc_start: 0.4326 (OUTLIER) cc_final: 0.3790 (m-80) REVERT: E 199 THR cc_start: 0.4233 (OUTLIER) cc_final: 0.3536 (t) REVERT: E 233 MET cc_start: -0.3048 (mpm) cc_final: -0.4476 (tpt) REVERT: E 270 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: E 280 LEU cc_start: 0.3322 (OUTLIER) cc_final: 0.2847 (tm) REVERT: E 306 TYR cc_start: 0.2816 (m-80) cc_final: 0.2568 (m-80) REVERT: E 315 ASP cc_start: 0.4190 (OUTLIER) cc_final: 0.3909 (t0) REVERT: E 350 SER cc_start: -0.0174 (OUTLIER) cc_final: -0.0867 (m) REVERT: E 497 ARG cc_start: 0.4140 (OUTLIER) cc_final: 0.3931 (mmt90) REVERT: E 578 ASP cc_start: 0.0742 (OUTLIER) cc_final: 0.0359 (p0) REVERT: G 3 GLU cc_start: 0.1235 (OUTLIER) cc_final: -0.0308 (mm-30) REVERT: G 10 ARG cc_start: 0.2555 (OUTLIER) cc_final: 0.1052 (tpm170) REVERT: G 32 TYR cc_start: 0.0459 (m-80) cc_final: -0.0439 (m-80) outliers start: 98 outliers final: 39 residues processed: 247 average time/residue: 0.9789 time to fit residues: 291.3770 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 : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 776 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 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 59 LEU 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 182 TRP 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 121 ILE 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 260 ASP Chi-restraints excluded: chain F residue 289 SER 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 570 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 280 LEU 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 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 588 THR 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 92 LYS Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 35 optimal weight: 0.0970 chunk 133 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 80 optimal weight: 0.0020 chunk 46 optimal weight: 0.0000 chunk 150 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 886 GLN ** 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** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.233939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.177836 restraints weight = 71807.998| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 4.51 r_work: 0.4160 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1880 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 22652 Z= 0.125 Angle : 0.675 15.554 31048 Z= 0.328 Chirality : 0.042 0.234 3601 Planarity : 0.004 0.053 3752 Dihedral : 12.314 81.329 3818 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.94 % Rotamer: Outliers : 4.35 % Allowed : 32.70 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2650 helix: 0.11 (0.17), residues: 972 sheet: -0.72 (0.37), residues: 211 loop : -2.16 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 598 HIS 0.013 0.001 HIS A 642 PHE 0.018 0.001 PHE A 348 TYR 0.021 0.001 TYR A 831 ARG 0.009 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 842) hydrogen bonds : angle 4.88617 ( 2324) metal coordination : bond 0.02347 ( 32) metal coordination : angle 4.30934 ( 27) covalent geometry : bond 0.00257 (22620) covalent geometry : angle 0.66330 (31021) *********************** 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 260 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 162 time to evaluate : 2.376 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: 0.1822 (OUTLIER) cc_final: 0.0384 (m170) REVERT: A 226 THR cc_start: 0.7833 (p) cc_final: 0.7425 (t) REVERT: A 239 SER cc_start: 0.1061 (OUTLIER) cc_final: 0.0599 (t) REVERT: A 601 MET cc_start: -0.2137 (mpt) cc_final: -0.2408 (mpp) REVERT: A 633 MET cc_start: 0.2002 (ttp) cc_final: -0.0567 (mpp) REVERT: A 666 MET cc_start: 0.0504 (OUTLIER) cc_final: 0.0005 (pmm) REVERT: A 767 ASN cc_start: 0.4852 (t0) cc_final: 0.4528 (t0) REVERT: A 875 GLN cc_start: 0.3126 (mp10) cc_final: 0.2746 (mt0) REVERT: A 889 ARG cc_start: 0.6675 (ttp80) cc_final: 0.6223 (ttm110) REVERT: B 79 LYS cc_start: 0.0598 (pptt) cc_final: -0.0986 (mtmt) REVERT: C 20 LEU cc_start: 0.5468 (tt) cc_final: 0.4856 (mp) REVERT: C 68 ILE cc_start: -0.2787 (OUTLIER) cc_final: -0.3009 (mm) REVERT: D 42 LEU cc_start: 0.0084 (OUTLIER) cc_final: -0.0365 (mt) REVERT: D 70 MET cc_start: 0.0543 (ptm) cc_final: -0.0239 (mtt) REVERT: D 139 LYS cc_start: 0.7145 (ttpp) cc_final: 0.6830 (tppt) REVERT: D 140 ASN cc_start: 0.6267 (m-40) cc_final: 0.5792 (t0) REVERT: D 182 TRP cc_start: 0.0208 (OUTLIER) cc_final: -0.0923 (m100) REVERT: F 75 HIS cc_start: -0.0367 (OUTLIER) cc_final: -0.2685 (t-90) REVERT: F 122 LEU cc_start: 0.6099 (tt) cc_final: 0.5662 (mt) REVERT: F 131 LYS cc_start: -0.0795 (OUTLIER) cc_final: -0.1264 (tptt) REVERT: F 185 TYR cc_start: 0.7181 (p90) cc_final: 0.6723 (p90) REVERT: F 202 LYS cc_start: 0.3300 (OUTLIER) cc_final: 0.3066 (mmmm) REVERT: F 248 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.3970 (tpm170) REVERT: F 289 SER cc_start: 0.1071 (OUTLIER) cc_final: 0.0802 (p) REVERT: F 526 LEU cc_start: -0.0491 (OUTLIER) cc_final: -0.0848 (pp) REVERT: F 576 MET cc_start: -0.3747 (OUTLIER) cc_final: -0.4355 (pp-130) REVERT: E 12 THR cc_start: -0.1045 (OUTLIER) cc_final: -0.1275 (t) REVERT: E 68 MET cc_start: 0.0262 (OUTLIER) cc_final: -0.0993 (pp-130) REVERT: E 73 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7941 (ttpp) REVERT: E 155 ARG cc_start: 0.1254 (mmt180) cc_final: 0.0637 (tpp80) REVERT: E 233 MET cc_start: -0.2788 (mpm) cc_final: -0.4255 (tpt) REVERT: E 270 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: E 280 LEU cc_start: 0.3226 (mt) cc_final: 0.2652 (tp) REVERT: E 306 TYR cc_start: 0.3126 (m-80) cc_final: 0.2904 (m-80) REVERT: E 315 ASP cc_start: 0.3914 (OUTLIER) cc_final: 0.3639 (t0) REVERT: E 350 SER cc_start: -0.0156 (OUTLIER) cc_final: -0.0812 (m) REVERT: E 436 MET cc_start: 0.0874 (pp-130) cc_final: 0.0569 (pp-130) REVERT: E 578 ASP cc_start: 0.0663 (OUTLIER) cc_final: 0.0296 (p0) REVERT: G 3 GLU cc_start: 0.1054 (OUTLIER) cc_final: -0.0674 (mm-30) REVERT: G 10 ARG cc_start: 0.2408 (OUTLIER) cc_final: 0.0867 (tpm170) REVERT: G 32 TYR cc_start: 0.0357 (m-80) cc_final: -0.0248 (m-80) outliers start: 98 outliers final: 45 residues processed: 239 average time/residue: 0.9890 time to fit residues: 283.5180 Evaluate side-chains 225 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 2.264 ------------------------------------------------------------------------------- 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 239 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 586 THR 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 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 VAL 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 153 LEU Chi-restraints excluded: chain C residue 22 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 182 TRP 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 121 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 202 LYS 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 422 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 588 THR 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 88 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 243 optimal weight: 0.5980 chunk 249 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 182 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 573 GLN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.237064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.182777 restraints weight = 59922.858| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 3.12 r_work: 0.4284 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4252 r_free = 0.4252 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4252 r_free = 0.4252 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2070 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 22652 Z= 0.149 Angle : 0.702 14.552 31048 Z= 0.348 Chirality : 0.043 0.283 3601 Planarity : 0.005 0.048 3752 Dihedral : 12.353 82.373 3818 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.40 % Favored : 91.41 % Rotamer: Outliers : 4.61 % Allowed : 32.75 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2650 helix: -0.01 (0.17), residues: 965 sheet: -0.82 (0.38), residues: 205 loop : -2.20 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 598 HIS 0.014 0.001 HIS A 642 PHE 0.041 0.002 PHE A 471 TYR 0.020 0.002 TYR A 831 ARG 0.007 0.001 ARG E 560 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 842) hydrogen bonds : angle 5.06596 ( 2324) metal coordination : bond 0.02686 ( 32) metal coordination : angle 4.45401 ( 27) covalent geometry : bond 0.00318 (22620) covalent geometry : angle 0.69035 (31021) *********************** 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 265 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 161 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.1870 (OUTLIER) cc_final: 0.0307 (m170) REVERT: A 226 THR cc_start: 0.8127 (p) cc_final: 0.7700 (t) REVERT: A 239 SER cc_start: 0.1279 (OUTLIER) cc_final: 0.0783 (t) REVERT: A 633 MET cc_start: 0.2287 (ttp) cc_final: -0.0434 (mpp) REVERT: A 666 MET cc_start: 0.0434 (OUTLIER) cc_final: -0.0247 (pmm) REVERT: A 874 ASN cc_start: 0.2996 (m110) cc_final: 0.2161 (t0) REVERT: A 889 ARG cc_start: 0.6794 (ttp80) cc_final: 0.6381 (ttm110) REVERT: B 79 LYS cc_start: 0.0407 (OUTLIER) cc_final: -0.1157 (mtmt) REVERT: C 68 ILE cc_start: -0.2781 (OUTLIER) cc_final: -0.3009 (mm) REVERT: D 42 LEU cc_start: 0.0007 (OUTLIER) cc_final: -0.0492 (mt) REVERT: D 55 MET cc_start: 0.2271 (mmp) cc_final: 0.2008 (mmm) REVERT: D 70 MET cc_start: 0.0661 (ptm) cc_final: -0.0209 (mtt) REVERT: D 182 TRP cc_start: 0.0095 (OUTLIER) cc_final: -0.1028 (m100) REVERT: F 75 HIS cc_start: -0.0687 (OUTLIER) cc_final: -0.3090 (t-90) REVERT: F 93 TYR cc_start: -0.0135 (m-80) cc_final: -0.2028 (m-80) REVERT: F 122 LEU cc_start: 0.6125 (tt) cc_final: 0.5691 (mt) REVERT: F 131 LYS cc_start: -0.0755 (OUTLIER) cc_final: -0.1240 (tptt) REVERT: F 185 TYR cc_start: 0.7260 (p90) cc_final: 0.6758 (p90) REVERT: F 248 ARG cc_start: 0.4977 (OUTLIER) cc_final: 0.4115 (tpm170) REVERT: F 289 SER cc_start: 0.1314 (OUTLIER) cc_final: 0.1043 (p) REVERT: F 526 LEU cc_start: -0.0292 (OUTLIER) cc_final: -0.0634 (pp) REVERT: F 576 MET cc_start: -0.3819 (OUTLIER) cc_final: -0.4345 (pp-130) REVERT: E 12 THR cc_start: -0.0814 (OUTLIER) cc_final: -0.1084 (t) REVERT: E 68 MET cc_start: 0.0640 (OUTLIER) cc_final: -0.0635 (pp-130) REVERT: E 73 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7918 (ttpp) REVERT: E 155 ARG cc_start: 0.1529 (mmt180) cc_final: 0.0857 (tpp80) REVERT: E 198 TYR cc_start: 0.4458 (OUTLIER) cc_final: 0.3967 (m-80) REVERT: E 226 VAL cc_start: 0.4553 (OUTLIER) cc_final: 0.4289 (t) REVERT: E 233 MET cc_start: -0.2726 (OUTLIER) cc_final: -0.4157 (tpt) REVERT: E 270 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: E 280 LEU cc_start: 0.3299 (mt) cc_final: 0.2753 (tm) REVERT: E 315 ASP cc_start: 0.4022 (OUTLIER) cc_final: 0.3768 (t0) REVERT: E 350 SER cc_start: 0.0068 (OUTLIER) cc_final: -0.0541 (m) REVERT: E 497 ARG cc_start: 0.4204 (OUTLIER) cc_final: 0.3974 (mmt90) REVERT: E 578 ASP cc_start: 0.0978 (OUTLIER) cc_final: 0.0647 (p0) REVERT: G 3 GLU cc_start: 0.1282 (OUTLIER) cc_final: -0.0497 (mm-30) REVERT: G 10 ARG cc_start: 0.2543 (OUTLIER) cc_final: 0.0903 (tpm170) REVERT: G 32 TYR cc_start: 0.0655 (m-80) cc_final: -0.0474 (m-80) outliers start: 104 outliers final: 50 residues processed: 244 average time/residue: 1.0653 time to fit residues: 311.1276 Evaluate side-chains 232 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 2.453 ------------------------------------------------------------------------------- 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 239 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 642 HIS 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 784 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 853 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 79 LYS 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 68 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 12 THR 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 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 422 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 270 GLN 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 440 THR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 70 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 17 optimal weight: 0.0670 chunk 232 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 overall best weight: 2.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 309 HIS A 314 ASN A 447 ASN A 459 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN A 882 HIS B 118 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.245445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.203131 restraints weight = 76293.878| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 4.44 r_work: 0.4465 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2642 moved from start: 0.7375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.177 22652 Z= 0.330 Angle : 1.066 16.531 31048 Z= 0.540 Chirality : 0.055 0.359 3601 Planarity : 0.007 0.080 3752 Dihedral : 13.131 89.153 3814 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.36 % Favored : 89.45 % Rotamer: Outliers : 5.53 % Allowed : 32.79 % Favored : 61.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.15), residues: 2650 helix: -1.02 (0.16), residues: 946 sheet: -1.45 (0.33), residues: 226 loop : -2.56 (0.14), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 268 HIS 0.021 0.003 HIS A 816 PHE 0.065 0.005 PHE A 471 TYR 0.055 0.003 TYR A 289 ARG 0.010 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.07282 ( 842) hydrogen bonds : angle 6.64835 ( 2324) metal coordination : bond 0.03960 ( 32) metal coordination : angle 5.77180 ( 27) covalent geometry : bond 0.00721 (22620) covalent geometry : angle 1.05241 (31021) *********************** 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 294 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 169 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2621 (OUTLIER) cc_final: 0.1018 (m170) REVERT: A 183 ARG cc_start: 0.1874 (OUTLIER) cc_final: 0.1215 (mtp180) REVERT: A 482 CYS cc_start: 0.2790 (OUTLIER) cc_final: 0.2384 (t) REVERT: A 633 MET cc_start: 0.2399 (ttp) cc_final: -0.0327 (mpp) REVERT: A 770 TYR cc_start: -0.0256 (OUTLIER) cc_final: -0.0886 (m-80) REVERT: A 889 ARG cc_start: 0.7239 (ttp80) cc_final: 0.6942 (ttm110) REVERT: B 79 LYS cc_start: 0.0361 (OUTLIER) cc_final: -0.1104 (mtmt) REVERT: B 129 MET cc_start: -0.0027 (ttp) cc_final: -0.0334 (ttp) REVERT: B 155 GLU cc_start: 0.4494 (pt0) cc_final: 0.4187 (mp0) REVERT: C 14 LEU cc_start: 0.1047 (OUTLIER) cc_final: -0.0473 (tp) REVERT: C 20 LEU cc_start: 0.4634 (tt) cc_final: 0.4163 (mp) REVERT: D 67 MET cc_start: -0.0357 (ttt) cc_final: -0.1463 (ptt) REVERT: F 75 HIS cc_start: -0.0807 (OUTLIER) cc_final: -0.3396 (t-90) REVERT: F 93 TYR cc_start: -0.0022 (m-80) cc_final: -0.2103 (m-80) REVERT: F 122 LEU cc_start: 0.6250 (tt) cc_final: 0.5800 (mt) REVERT: F 185 TYR cc_start: 0.7348 (p90) cc_final: 0.6875 (p90) REVERT: F 248 ARG cc_start: 0.4861 (OUTLIER) cc_final: 0.3960 (tpm170) REVERT: F 289 SER cc_start: 0.1345 (OUTLIER) cc_final: 0.1094 (p) REVERT: F 526 LEU cc_start: -0.0100 (OUTLIER) cc_final: -0.0459 (pp) REVERT: F 576 MET cc_start: -0.3521 (OUTLIER) cc_final: -0.4262 (pp-130) REVERT: E 12 THR cc_start: -0.1056 (OUTLIER) cc_final: -0.1509 (m) REVERT: E 68 MET cc_start: 0.0465 (OUTLIER) cc_final: -0.0522 (pp-130) REVERT: E 73 LYS cc_start: 0.8410 (mppt) cc_final: 0.7957 (ttpp) REVERT: E 198 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.3935 (m-80) REVERT: E 226 VAL cc_start: 0.4444 (OUTLIER) cc_final: 0.4144 (t) REVERT: E 233 MET cc_start: -0.2012 (OUTLIER) cc_final: -0.3810 (tpt) REVERT: E 270 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6561 (mp10) REVERT: E 280 LEU cc_start: 0.3239 (mt) cc_final: 0.2622 (tm) REVERT: E 306 TYR cc_start: 0.3662 (m-80) cc_final: 0.3418 (m-10) REVERT: E 315 ASP cc_start: 0.4061 (OUTLIER) cc_final: 0.3800 (t0) REVERT: E 350 SER cc_start: 0.0317 (OUTLIER) cc_final: -0.0287 (m) REVERT: E 364 PRO cc_start: 0.5011 (Cg_exo) cc_final: 0.4768 (Cg_endo) REVERT: E 497 ARG cc_start: 0.4034 (OUTLIER) cc_final: 0.3798 (mmt90) REVERT: E 578 ASP cc_start: 0.1041 (OUTLIER) cc_final: 0.0626 (p0) REVERT: G 2 ASN cc_start: 0.0916 (OUTLIER) cc_final: 0.0481 (p0) REVERT: G 3 GLU cc_start: 0.1215 (OUTLIER) cc_final: -0.0685 (mm-30) REVERT: G 10 ARG cc_start: 0.2531 (OUTLIER) cc_final: 0.0971 (tpm170) REVERT: G 74 ARG cc_start: 0.4800 (ttm-80) cc_final: 0.4166 (ttp80) outliers start: 125 outliers final: 57 residues processed: 264 average time/residue: 0.9784 time to fit residues: 309.5126 Evaluate side-chains 234 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 153 time to evaluate : 2.233 ------------------------------------------------------------------------------- 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 113 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 514 LEU 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 632 ILE Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 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 79 LYS 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 36 HIS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 16 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 75 HIS 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 422 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 270 GLN 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 440 THR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 110 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 142 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 137 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 240 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 314 ASN A 447 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 GLN ** 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 557 ASN E 46 ASN ** E 116 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 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.247553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.207019 restraints weight = 89304.518| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 4.80 r_work: 0.4525 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4504 r_free = 0.4504 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4504 r_free = 0.4504 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2684 moved from start: 0.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 22652 Z= 0.268 Angle : 0.965 14.577 31048 Z= 0.483 Chirality : 0.052 0.389 3601 Planarity : 0.007 0.080 3752 Dihedral : 13.064 85.539 3814 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.87 % Favored : 89.90 % Rotamer: Outliers : 4.04 % Allowed : 34.90 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.15), residues: 2650 helix: -1.18 (0.16), residues: 948 sheet: -1.72 (0.34), residues: 218 loop : -2.62 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 268 HIS 0.015 0.002 HIS A 872 PHE 0.045 0.004 PHE A 843 TYR 0.049 0.003 TYR A 289 ARG 0.007 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.06439 ( 842) hydrogen bonds : angle 6.51951 ( 2324) metal coordination : bond 0.03285 ( 32) metal coordination : angle 5.33575 ( 27) covalent geometry : bond 0.00585 (22620) covalent geometry : angle 0.95283 (31021) *********************** 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 254 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 163 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.4272 (OUTLIER) cc_final: 0.3258 (mp10) REVERT: A 113 HIS cc_start: 0.2522 (OUTLIER) cc_final: 0.1161 (m170) REVERT: A 162 TRP cc_start: 0.2635 (p-90) cc_final: 0.2376 (p90) REVERT: A 294 TYR cc_start: 0.5049 (OUTLIER) cc_final: 0.4358 (t80) REVERT: A 411 LYS cc_start: 0.2327 (mtmt) cc_final: 0.1969 (mmmt) REVERT: A 606 TYR cc_start: 0.6894 (m-10) cc_final: 0.6353 (m-10) REVERT: A 633 MET cc_start: 0.2636 (ttp) cc_final: -0.0276 (mpm) REVERT: A 770 TYR cc_start: -0.0329 (OUTLIER) cc_final: -0.1900 (m-10) REVERT: A 835 SER cc_start: 0.8206 (t) cc_final: 0.7983 (m) REVERT: A 889 ARG cc_start: 0.7464 (ttp80) cc_final: 0.6526 (ttm170) REVERT: B 79 LYS cc_start: 0.0694 (OUTLIER) cc_final: -0.0816 (mtmt) REVERT: B 147 PHE cc_start: 0.3710 (p90) cc_final: 0.3056 (p90) REVERT: B 155 GLU cc_start: 0.4458 (pt0) cc_final: 0.4224 (mp0) REVERT: B 176 ASN cc_start: 0.5848 (t0) cc_final: 0.5112 (m-40) REVERT: C 14 LEU cc_start: 0.1112 (OUTLIER) cc_final: -0.0725 (tp) REVERT: D 67 MET cc_start: -0.0281 (ttt) cc_final: -0.1346 (ptt) REVERT: D 137 THR cc_start: 0.3584 (m) cc_final: 0.3358 (p) REVERT: F 93 TYR cc_start: 0.0012 (m-80) cc_final: -0.2226 (m-80) REVERT: F 122 LEU cc_start: 0.6265 (tt) cc_final: 0.5813 (mt) REVERT: F 185 TYR cc_start: 0.7367 (p90) cc_final: 0.6914 (p90) REVERT: F 248 ARG cc_start: 0.4995 (OUTLIER) cc_final: 0.3932 (tpm170) REVERT: F 289 SER cc_start: 0.1384 (OUTLIER) cc_final: 0.1163 (p) REVERT: F 526 LEU cc_start: -0.0176 (OUTLIER) cc_final: -0.0505 (pp) REVERT: E 122 LEU cc_start: 0.5345 (pp) cc_final: 0.4994 (pt) REVERT: E 198 TYR cc_start: 0.4446 (OUTLIER) cc_final: 0.3819 (m-80) REVERT: E 226 VAL cc_start: 0.4548 (OUTLIER) cc_final: 0.4258 (t) REVERT: E 233 MET cc_start: -0.1984 (OUTLIER) cc_final: -0.3827 (tpt) REVERT: E 270 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6487 (mp10) REVERT: E 280 LEU cc_start: 0.3400 (mt) cc_final: 0.2690 (tm) REVERT: E 315 ASP cc_start: 0.3922 (OUTLIER) cc_final: 0.3676 (t0) REVERT: E 350 SER cc_start: 0.0173 (OUTLIER) cc_final: -0.0345 (m) REVERT: E 497 ARG cc_start: 0.4040 (OUTLIER) cc_final: 0.3747 (mmt90) REVERT: E 578 ASP cc_start: 0.0868 (OUTLIER) cc_final: 0.0334 (p0) REVERT: G 3 GLU cc_start: 0.1361 (OUTLIER) cc_final: -0.0130 (mm-30) REVERT: G 10 ARG cc_start: 0.2599 (OUTLIER) cc_final: 0.1128 (tpm170) REVERT: G 74 ARG cc_start: 0.4558 (ttm-80) cc_final: 0.4142 (tmt-80) outliers start: 91 outliers final: 55 residues processed: 238 average time/residue: 0.9887 time to fit residues: 285.0047 Evaluate side-chains 228 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 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 285 ARG Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 329 LEU 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 514 LEU 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 632 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 833 ASP 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 79 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 ILE 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 36 HIS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 121 ILE 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 422 PHE Chi-restraints excluded: chain F residue 526 LEU 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 198 TYR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER 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 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 45 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 247 optimal weight: 0.0370 chunk 122 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 447 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** 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 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** 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 = 0.5068 r_free = 0.5068 target = 0.248177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.208022 restraints weight = 81067.590| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 3.55 r_work: 0.4548 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4538 r_free = 0.4538 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4538 r_free = 0.4538 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2640 moved from start: 0.8129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 22652 Z= 0.190 Angle : 0.844 14.846 31048 Z= 0.422 Chirality : 0.047 0.282 3601 Planarity : 0.006 0.078 3752 Dihedral : 12.875 82.924 3814 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.91 % Favored : 89.86 % Rotamer: Outliers : 3.60 % Allowed : 35.73 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.15), residues: 2650 helix: -1.03 (0.16), residues: 961 sheet: -1.77 (0.31), residues: 258 loop : -2.56 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 598 HIS 0.010 0.002 HIS A 642 PHE 0.036 0.003 PHE A 745 TYR 0.038 0.002 TYR A 289 ARG 0.009 0.001 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.05801 ( 842) hydrogen bonds : angle 6.15030 ( 2324) metal coordination : bond 0.02787 ( 32) metal coordination : angle 4.97989 ( 27) covalent geometry : bond 0.00412 (22620) covalent geometry : angle 0.83189 (31021) ********************** 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 244 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 163 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.4388 (OUTLIER) cc_final: 0.3352 (mp10) REVERT: A 113 HIS cc_start: 0.2674 (OUTLIER) cc_final: 0.1208 (m170) REVERT: A 162 TRP cc_start: 0.2581 (p-90) cc_final: 0.2359 (p90) REVERT: A 226 THR cc_start: 0.8225 (p) cc_final: 0.7948 (t) REVERT: A 411 LYS cc_start: 0.2367 (mtmt) cc_final: 0.1976 (mmmt) REVERT: A 463 MET cc_start: 0.1945 (mmt) cc_final: 0.1094 (mmt) REVERT: A 566 MET cc_start: 0.2519 (mmt) cc_final: 0.1490 (mtt) REVERT: A 606 TYR cc_start: 0.6624 (m-10) cc_final: 0.6265 (m-10) REVERT: A 633 MET cc_start: 0.2573 (ttp) cc_final: 0.0048 (mpm) REVERT: A 835 SER cc_start: 0.8072 (t) cc_final: 0.7818 (m) REVERT: A 855 MET cc_start: 0.0559 (pmm) cc_final: 0.0309 (ppp) REVERT: A 889 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6286 (ttm170) REVERT: A 924 MET cc_start: 0.3392 (tpt) cc_final: 0.2434 (tpt) REVERT: B 79 LYS cc_start: 0.0631 (OUTLIER) cc_final: -0.1030 (mtmt) REVERT: B 147 PHE cc_start: 0.3763 (p90) cc_final: 0.3220 (p90) REVERT: B 155 GLU cc_start: 0.4717 (pt0) cc_final: 0.4433 (mp0) REVERT: B 176 ASN cc_start: 0.5910 (t0) cc_final: 0.5089 (m-40) REVERT: C 14 LEU cc_start: 0.1124 (OUTLIER) cc_final: -0.0764 (tp) REVERT: C 20 LEU cc_start: 0.4003 (OUTLIER) cc_final: 0.3668 (mp) REVERT: D 67 MET cc_start: -0.0307 (ttt) cc_final: -0.1394 (ptt) REVERT: F 93 TYR cc_start: -0.0008 (m-80) cc_final: -0.2298 (m-80) REVERT: F 122 LEU cc_start: 0.6226 (tt) cc_final: 0.5769 (mp) REVERT: F 176 LEU cc_start: 0.2365 (tm) cc_final: 0.2073 (tp) REVERT: F 185 TYR cc_start: 0.7454 (p90) cc_final: 0.6995 (p90) REVERT: F 248 ARG cc_start: 0.5033 (OUTLIER) cc_final: 0.3981 (tpm170) REVERT: F 274 MET cc_start: 0.7123 (ptm) cc_final: 0.6571 (ppp) REVERT: F 289 SER cc_start: 0.1822 (OUTLIER) cc_final: 0.1589 (p) REVERT: F 526 LEU cc_start: 0.0142 (OUTLIER) cc_final: -0.0169 (pp) REVERT: E 122 LEU cc_start: 0.5239 (pp) cc_final: 0.5015 (pt) REVERT: E 198 TYR cc_start: 0.4487 (OUTLIER) cc_final: 0.3797 (m-80) REVERT: E 226 VAL cc_start: 0.4513 (OUTLIER) cc_final: 0.4247 (t) REVERT: E 233 MET cc_start: -0.2048 (OUTLIER) cc_final: -0.3822 (tpt) REVERT: E 270 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: E 280 LEU cc_start: 0.3281 (mt) cc_final: 0.2586 (tm) REVERT: E 306 TYR cc_start: 0.3880 (m-10) cc_final: 0.3547 (m-10) REVERT: E 315 ASP cc_start: 0.3944 (OUTLIER) cc_final: 0.3700 (t0) REVERT: E 350 SER cc_start: 0.0418 (OUTLIER) cc_final: -0.0067 (m) REVERT: E 497 ARG cc_start: 0.4120 (OUTLIER) cc_final: 0.3797 (mmt90) REVERT: E 578 ASP cc_start: 0.1195 (OUTLIER) cc_final: 0.0808 (p0) REVERT: G 3 GLU cc_start: 0.0975 (OUTLIER) cc_final: -0.0616 (mm-30) REVERT: G 10 ARG cc_start: 0.2478 (OUTLIER) cc_final: 0.1082 (tpm170) REVERT: G 74 ARG cc_start: 0.4607 (ttm-80) cc_final: 0.4095 (ttp80) outliers start: 81 outliers final: 53 residues processed: 231 average time/residue: 0.9797 time to fit residues: 271.6250 Evaluate side-chains 229 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 158 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 113 HIS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 329 LEU 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 514 LEU 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 632 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 784 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 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 79 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS 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 422 PHE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 526 LEU 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 198 TYR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 350 SER 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 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 91 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 174 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 226 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 195 optimal weight: 0.0980 chunk 201 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 198 optimal weight: 30.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS ** 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 G 2 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.247370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.208645 restraints weight = 88763.667| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 4.85 r_work: 0.4443 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4458 r_free = 0.4458 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4458 r_free = 0.4458 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2598 moved from start: 0.8282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 22652 Z= 0.158 Angle : 0.776 15.248 31048 Z= 0.383 Chirality : 0.045 0.277 3601 Planarity : 0.005 0.079 3752 Dihedral : 12.577 78.839 3814 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.55 % Favored : 91.26 % Rotamer: Outliers : 3.60 % Allowed : 35.56 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2650 helix: -0.80 (0.16), residues: 972 sheet: -1.68 (0.32), residues: 261 loop : -2.43 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 154 HIS 0.007 0.001 HIS A 642 PHE 0.030 0.002 PHE A 745 TYR 0.030 0.002 TYR A 831 ARG 0.005 0.001 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 842) hydrogen bonds : angle 5.74496 ( 2324) metal coordination : bond 0.03591 ( 32) metal coordination : angle 4.84778 ( 27) covalent geometry : bond 0.00335 (22620) covalent geometry : angle 0.76338 (31021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25560.12 seconds wall clock time: 438 minutes 21.02 seconds (26301.02 seconds total)