Starting phenix.real_space_refine on Tue Apr 7 20:49:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eiz_31146/04_2026/7eiz_31146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eiz_31146/04_2026/7eiz_31146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eiz_31146/04_2026/7eiz_31146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eiz_31146/04_2026/7eiz_31146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eiz_31146/04_2026/7eiz_31146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eiz_31146/04_2026/7eiz_31146.map" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4911 atoms to isotropic. 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 13 6.06 5 P 52 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 17003 2.51 5 N 4589 2.21 5 O 5217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27083 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "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: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 121} 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: "K" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4169 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PTRANS': 26, 'TRANS': 492} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4544 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 587, 4536 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 30, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 587, 4536 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 30, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 4630 Chain: "F" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 60.996 66.855 136.037 1.00 83.57 S ATOM 2487 SG CYS A 306 62.049 66.977 132.333 1.00 81.60 S ATOM 2519 SG CYS A 310 58.387 67.630 133.492 1.00 84.82 S ATOM 3927 SG CYS A 487 76.838 73.496 148.904 1.00104.54 S ATOM 5180 SG CYS A 645 78.370 74.130 145.440 1.00111.67 S ATOM 5186 SG CYS A 646 74.877 72.679 145.657 1.00109.79 S ATOM 12209 SG CYS H 74 34.977 41.672 72.016 1.001115.8 S ATOM 12235 SG CYS H 77 34.468 44.915 73.953 1.001115.8 S ATOM 12340 SG CYS H 90 31.691 42.643 72.436 1.001115.8 S ATOM 12543 SG CYS H 117 20.470 30.481 67.114 1.001115.8 S ATOM 12563 SG CYS H 120 19.161 28.097 68.388 1.001115.8 S ATOM 12636 SG CYS H 130 19.173 27.592 64.144 1.001115.8 S ATOM 15371 SG CYS K 207 52.035 53.449 49.079 1.001115.8 S ATOM 15391 SG CYS K 210 52.406 55.467 45.813 1.001115.8 S ATOM 15512 SG CYS K 226 54.713 56.174 48.788 1.001115.8 S ATOM 15812 SG CYS K 261 78.342 64.123 70.847 1.001115.8 S ATOM 15942 SG CYS K 279 76.594 62.306 67.962 1.001115.8 S ATOM 17332 SG CYS K 452 95.920 69.392 17.263 1.001115.8 S ATOM 17559 SG CYS K 484 95.211 70.824 18.891 1.001115.8 S ATOM 18027 SG CYS E 16 91.439 63.605 189.565 1.00168.77 S ATOM 18042 SG CYS E 19 89.998 60.614 191.673 1.00185.20 S ATOM 17945 SG CYS E 5 86.633 73.645 196.724 1.00179.03 S ATOM 17966 SG CYS E 8 89.505 72.889 199.281 1.00198.99 S ATOM 18104 SG CYS E 26 90.362 74.842 196.802 1.00190.40 S ATOM 18121 SG CYS E 29 90.114 71.458 196.040 1.00196.44 S ATOM 18286 SG CYS E 50 101.440 68.975 173.822 1.00376.96 S ATOM 18316 SG CYS E 55 104.012 67.480 171.411 1.00428.48 S ATOM 18449 SG CYS E 72 104.901 70.062 173.572 1.00405.88 S ATOM 22494 SG CYS F 5 73.723 116.597 200.812 1.00305.30 S ATOM 22515 SG CYS F 8 75.244 118.869 200.395 1.00327.27 S ATOM 22653 SG CYS F 26 77.659 117.250 199.694 1.00297.40 S ATOM 22674 SG CYS F 29 76.811 117.315 203.331 1.00318.37 S ATOM 22839 SG CYS F 50 85.492 93.854 192.475 1.00334.74 S ATOM 22869 SG CYS F 55 87.324 90.548 193.304 1.00378.87 S ATOM 23002 SG CYS F 72 88.871 93.868 193.909 1.00333.77 S ATOM 22576 SG CYS F 16 75.073 105.818 202.911 1.00268.87 S ATOM 22591 SG CYS F 19 71.963 106.212 205.070 1.00289.75 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET E 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.59 Time building chain proxies: 6.05, per 1000 atoms: 0.22 Number of scatterers: 27083 At special positions: 0 Unit cell: (145.22, 151.58, 260.76, 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 13 29.99 S 208 16.00 P 52 15.00 Mg 1 11.99 O 5217 8.00 N 4589 7.00 C 17003 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: 2.08 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " 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 26 " 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 E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 29 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 26 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 55 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 19 " pdb=" ZN H 200 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 77 " pdb="ZN ZN H 200 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 74 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 90 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 120 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 117 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" ND1 HIS K 229 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 226 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 210 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 207 " pdb=" ZN K 602 " pdb="ZN ZN K 602 " - pdb=" NE2 HIS K 264 " pdb="ZN ZN K 602 " - pdb=" NE2 HIS K 257 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 261 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 279 " pdb=" ZN K 603 " pdb="ZN ZN K 603 " - pdb=" ND1 HIS K 487 " pdb="ZN ZN K 603 " - pdb=" SG CYS K 452 " pdb="ZN ZN K 603 " - pdb=" SG CYS K 484 " Number of angles added : 34 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6296 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 29 sheets defined 38.6% alpha, 10.5% beta 17 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.651A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.714A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 199 removed outlier: 3.647A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 4.803A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.972A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.652A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.616A pdb=" N LEU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 4.416A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.575A pdb=" N GLN A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.034A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.801A pdb=" N ALA A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 626' Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.660A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.839A pdb=" N THR A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.813A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.729A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.599A pdb=" N LEU A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.689A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.772A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.525A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.794A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.555A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.659A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.568A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.801A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 82 removed outlier: 5.071A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 removed outlier: 4.225A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 22 through 32 Processing helix chain 'H' and resid 74 through 79 Processing helix chain 'H' and resid 106 through 114 removed outlier: 3.943A pdb=" N PHE H 110 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 143 through 153 removed outlier: 4.337A pdb=" N HIS K 148 " --> pdb=" O GLN K 145 " (cutoff:3.500A) Proline residue: K 151 - end of helix Processing helix chain 'K' and resid 158 through 174 removed outlier: 3.898A pdb=" N VAL K 162 " --> pdb=" O PRO K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 196 removed outlier: 4.259A pdb=" N GLU K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYS K 196 " --> pdb=" O LEU K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 199 No H-bonds generated for 'chain 'K' and resid 197 through 199' Processing helix chain 'K' and resid 252 through 261 removed outlier: 4.457A pdb=" N TYR K 260 " --> pdb=" O ASN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 287 removed outlier: 4.041A pdb=" N ALA K 274 " --> pdb=" O ALA K 270 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS K 285 " --> pdb=" O ALA K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 325 removed outlier: 3.976A pdb=" N ILE K 305 " --> pdb=" O ASP K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 502 removed outlier: 3.728A pdb=" N ILE K 502 " --> pdb=" O TYR K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 516 through 523 removed outlier: 3.708A pdb=" N TRP K 520 " --> pdb=" O THR K 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.688A pdb=" N THR E 37 " --> pdb=" O HIS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.632A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 146 Processing helix chain 'E' and resid 259 through 270 removed outlier: 3.999A pdb=" N SER E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASN E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN E 268 " --> pdb=" O SER E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 312 through 325 removed outlier: 4.451A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 379 Processing helix chain 'E' and resid 380 through 389 removed outlier: 4.049A pdb=" N ASN E 388 " --> pdb=" O LEU E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 430 Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.967A pdb=" N THR E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 502 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.576A pdb=" N TRP E 506 " --> pdb=" O ASN E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 524 Processing helix chain 'E' and resid 552 through 557 removed outlier: 4.002A pdb=" N ASN E 557 " --> pdb=" O ALA E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 564 Processing helix chain 'E' and resid 579 through 585 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 72 through 76 removed outlier: 3.815A pdb=" N HIS F 75 " --> pdb=" O CYS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 116 through 124 Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 275 removed outlier: 4.152A pdb=" N GLY F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET F 274 " --> pdb=" O GLN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 311 through 325 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 359 through 363 Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 433 Processing helix chain 'F' and resid 445 through 455 removed outlier: 3.649A pdb=" N ALA F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 500 Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.824A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 557 Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 578 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 59 removed outlier: 4.827A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 343 removed outlier: 3.605A pdb=" N VAL B 115 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA5, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.668A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 540 through 544 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.974A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.625A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 67 through 68 removed outlier: 3.777A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG G 10 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA G 16 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP G 26 " --> pdb=" O ALA G 16 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N ASN G 27 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N SER G 46 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU G 29 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU G 44 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 66 through 69 Processing sheet with id=AB4, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB5, first strand: chain 'K' and resid 116 through 118 removed outlier: 6.287A pdb=" N CYS K 94 " --> pdb=" O PRO K 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN K 108 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE K 89 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N PHE K 183 " --> pdb=" O ILE K 242 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 328 through 329 Processing sheet with id=AB7, first strand: chain 'K' and resid 351 through 352 removed outlier: 3.797A pdb=" N ASP K 352 " --> pdb=" O GLU K 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 382 through 385 removed outlier: 4.034A pdb=" N ILE K 397 " --> pdb=" O CYS K 382 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL K 398 " --> pdb=" O TRP K 509 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP K 509 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 410 through 411 Processing sheet with id=AC1, first strand: chain 'E' and resid 69 through 71 removed outlier: 3.513A pdb=" N SER E 69 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 192 through 198 removed outlier: 5.752A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.629A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 530 through 532 removed outlier: 3.798A pdb=" N THR E 547 " --> pdb=" O ILE E 512 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS E 473 " --> pdb=" O LEU E 590 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 4 removed outlier: 3.894A pdb=" N GLY F 3 " --> pdb=" O THR F 12 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AC8, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 156 removed outlier: 7.229A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 152 " --> pdb=" O PHE F 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.410A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ASP F 374 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR F 307 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN F 281 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 471 through 474 removed outlier: 7.373A pdb=" N TYR F 541 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY F 571 " --> pdb=" O TYR F 541 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR F 543 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU F 573 " --> pdb=" O TYR F 543 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE F 545 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE F 575 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6663 1.33 - 1.45: 6763 1.45 - 1.58: 13980 1.58 - 1.70: 96 1.70 - 1.82: 289 Bond restraints: 27791 Sorted by residual: bond pdb=" CA TYR A 455 " pdb=" C TYR A 455 " ideal model delta sigma weight residual 1.522 1.406 0.116 1.43e-02 4.89e+03 6.53e+01 bond pdb=" CA ASN A 403 " pdb=" C ASN A 403 " ideal model delta sigma weight residual 1.526 1.422 0.104 1.31e-02 5.83e+03 6.28e+01 bond pdb=" C VAL F 232 " pdb=" N MET F 233 " ideal model delta sigma weight residual 1.327 1.244 0.083 1.39e-02 5.18e+03 3.56e+01 bond pdb=" CA ARG A 10 " pdb=" C ARG A 10 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.38e-02 5.25e+03 2.24e+01 bond pdb=" C ASP A 618 " pdb=" N TYR A 619 " ideal model delta sigma weight residual 1.332 1.266 0.066 1.44e-02 4.82e+03 2.08e+01 ... (remaining 27786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 37448 3.67 - 7.33: 512 7.33 - 11.00: 39 11.00 - 14.67: 11 14.67 - 18.33: 3 Bond angle restraints: 38013 Sorted by residual: angle pdb=" C GLY A 503 " pdb=" N PHE A 504 " pdb=" CA PHE A 504 " ideal model delta sigma weight residual 122.67 107.48 15.19 2.19e+00 2.09e-01 4.81e+01 angle pdb=" C ASP A 845 " pdb=" N ASP A 846 " pdb=" CA ASP A 846 " ideal model delta sigma weight residual 121.54 108.52 13.02 1.91e+00 2.74e-01 4.65e+01 angle pdb=" C GLY F 527 " pdb=" N LEU F 528 " pdb=" CA LEU F 528 " ideal model delta sigma weight residual 120.94 133.38 -12.44 1.90e+00 2.77e-01 4.29e+01 angle pdb=" N PRO H 84 " pdb=" CA PRO H 84 " pdb=" C PRO H 84 " ideal model delta sigma weight residual 114.92 107.58 7.34 1.19e+00 7.06e-01 3.81e+01 angle pdb=" C LEU A 302 " pdb=" CA LEU A 302 " pdb=" CB LEU A 302 " ideal model delta sigma weight residual 117.07 108.94 8.13 1.44e+00 4.82e-01 3.19e+01 ... (remaining 38008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 15704 25.89 - 51.79: 822 51.79 - 77.68: 144 77.68 - 103.57: 10 103.57 - 129.46: 1 Dihedral angle restraints: 16681 sinusoidal: 6907 harmonic: 9774 Sorted by residual: dihedral pdb=" CA THR A 246 " pdb=" C THR A 246 " pdb=" N LEU A 247 " pdb=" CA LEU A 247 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA ARG F 442 " pdb=" C ARG F 442 " pdb=" N ARG F 443 " pdb=" CA ARG F 443 " ideal model delta harmonic sigma weight residual -180.00 -146.84 -33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA VAL A 848 " pdb=" C VAL A 848 " pdb=" N LYS A 849 " pdb=" CA LYS A 849 " ideal model delta harmonic sigma weight residual 180.00 147.44 32.56 0 5.00e+00 4.00e-02 4.24e+01 ... (remaining 16678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3033 0.054 - 0.107: 1053 0.107 - 0.161: 228 0.161 - 0.214: 27 0.214 - 0.268: 6 Chirality restraints: 4347 Sorted by residual: chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA TYR A 455 " pdb=" N TYR A 455 " pdb=" C TYR A 455 " pdb=" CB TYR A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ASP A 846 " pdb=" N ASP A 846 " pdb=" C ASP A 846 " pdb=" CB ASP A 846 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4344 not shown) Planarity restraints: 4671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.106 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO B 183 " -0.271 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 295 " 0.007 2.00e-02 2.50e+03 2.92e-02 1.28e+01 pdb=" CG HIS A 295 " 0.014 2.00e-02 2.50e+03 pdb=" ND1 HIS A 295 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 295 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS A 295 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS A 295 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 829 " -0.051 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO A 830 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 830 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 830 " -0.041 5.00e-02 4.00e+02 ... (remaining 4668 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 779 2.58 - 3.16: 27663 3.16 - 3.74: 44741 3.74 - 4.32: 60702 4.32 - 4.90: 92541 Nonbonded interactions: 226426 Sorted by model distance: nonbonded pdb=" O MET E 576 " pdb=" NH2 ARG E 579 " model vdw 1.999 3.120 nonbonded pdb=" O2 C I 19 " pdb=" N2 G J 41 " model vdw 2.012 2.496 nonbonded pdb=" OD2 ASP A 218 " pdb=" ND2 ASN G 1 " model vdw 2.029 3.120 nonbonded pdb=" O PRO E 283 " pdb=" NZ LYS E 288 " model vdw 2.041 3.120 nonbonded pdb=" SG CYS K 261 " pdb=" ND1 HIS K 264 " model vdw 2.056 3.480 ... (remaining 226421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 590 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 93 or (resid 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 100 or (resid 101 thro \ ugh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 th \ rough 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) \ or resid 203 or (resid 204 through 205 and (name N or name CA or name C or name \ O or name CB )) or resid 206 through 336 or resid 342 through 391 or (resid 392 \ through 393 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 94 through 473 or resid 475 through 523 or (resid 524 and (name N or name CA or \ name C or name O or name CB )) or resid 525 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.750 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.014 0.429 27841 Z= 0.615 Angle : 1.243 42.836 38047 Z= 0.662 Chirality : 0.055 0.268 4347 Planarity : 0.007 0.157 4671 Dihedral : 15.999 129.463 10385 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 38.94 Ramachandran Plot: Outliers : 0.61 % Allowed : 21.55 % Favored : 77.85 % Rotamer: Outliers : 0.77 % Allowed : 11.75 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.75 (0.10), residues: 3298 helix: -3.46 (0.10), residues: 1083 sheet: -3.13 (0.22), residues: 369 loop : -4.39 (0.11), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 51 TYR 0.042 0.003 TYR A 156 PHE 0.037 0.004 PHE A 321 TRP 0.017 0.003 TRP K 509 HIS 0.044 0.003 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.01283 (27791) covalent geometry : angle 1.17077 (38013) hydrogen bonds : bond 0.19435 ( 1010) hydrogen bonds : angle 9.22828 ( 2757) metal coordination : bond 0.10909 ( 50) metal coordination : angle 13.97772 ( 34) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.907 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 668 MET cc_start: 0.9113 (tmm) cc_final: 0.8878 (tmm) REVERT: B 49 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: B 55 MET cc_start: 0.9608 (mtp) cc_final: 0.9294 (mmm) REVERT: B 90 MET cc_start: 0.9526 (tmm) cc_final: 0.9253 (tmm) REVERT: B 174 MET cc_start: 0.8798 (tpt) cc_final: 0.8557 (tpp) REVERT: D 32 GLU cc_start: 0.8387 (tp30) cc_final: 0.7983 (pp20) REVERT: K 57 MET cc_start: 0.1754 (mmt) cc_final: 0.1328 (mpp) REVERT: K 241 MET cc_start: 0.0108 (mtm) cc_final: -0.0133 (mpp) REVERT: E 233 MET cc_start: 0.8665 (mmt) cc_final: 0.8169 (ppp) REVERT: E 436 MET cc_start: 0.6225 (mpp) cc_final: 0.6002 (mpp) REVERT: F 189 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8180 (tmtt) outliers start: 20 outliers final: 9 residues processed: 168 average time/residue: 0.2040 time to fit residues: 52.6624 Evaluate side-chains 116 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain K residue 74 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0010 chunk 298 optimal weight: 0.4980 overall best weight: 2.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 168 ASN A 210 GLN A 256 HIS ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN B 65 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN H 65 GLN K 22 GLN K 104 ASN E 164 HIS E 268 ASN E 361 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 GLN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.123593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.084621 restraints weight = 166529.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076733 restraints weight = 120447.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.074811 restraints weight = 101625.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.074709 restraints weight = 75041.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074062 restraints weight = 60479.601| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 27841 Z= 0.227 Angle : 0.852 23.691 38047 Z= 0.428 Chirality : 0.047 0.236 4347 Planarity : 0.006 0.140 4671 Dihedral : 12.723 127.132 4451 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.08 % Favored : 87.62 % Rotamer: Outliers : 2.67 % Allowed : 14.56 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.13), residues: 3298 helix: -1.61 (0.14), residues: 1128 sheet: -2.59 (0.24), residues: 373 loop : -3.60 (0.12), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 560 TYR 0.031 0.002 TYR F 299 PHE 0.022 0.002 PHE B 15 TRP 0.020 0.002 TRP E 167 HIS 0.012 0.002 HIS K 264 Details of bonding type rmsd covalent geometry : bond 0.00489 (27791) covalent geometry : angle 0.80929 (38013) hydrogen bonds : bond 0.06913 ( 1010) hydrogen bonds : angle 6.64844 ( 2757) metal coordination : bond 0.03130 ( 50) metal coordination : angle 8.93054 ( 34) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 130 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8242 (mmm) cc_final: 0.7832 (tpp) REVERT: A 402 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9065 (p) REVERT: A 454 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8959 (t0) REVERT: A 668 MET cc_start: 0.9013 (tmm) cc_final: 0.8436 (ttp) REVERT: A 906 MET cc_start: 0.7847 (tmm) cc_final: 0.7586 (tmm) REVERT: B 62 MET cc_start: 0.8627 (ppp) cc_final: 0.8194 (ppp) REVERT: B 174 MET cc_start: 0.8830 (tpt) cc_final: 0.8549 (tpp) REVERT: K 57 MET cc_start: 0.2933 (mmt) cc_final: 0.2208 (mpp) REVERT: K 195 MET cc_start: 0.0124 (mtt) cc_final: -0.0088 (mtt) REVERT: K 241 MET cc_start: -0.1349 (mtm) cc_final: -0.1652 (mpp) REVERT: E 429 MET cc_start: 0.8232 (mmm) cc_final: 0.7962 (mtp) outliers start: 74 outliers final: 34 residues processed: 201 average time/residue: 0.1744 time to fit residues: 56.7362 Evaluate side-chains 143 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 254 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 232 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 231 optimal weight: 40.0000 chunk 239 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 270 optimal weight: 0.1980 chunk 199 optimal weight: 40.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.122929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.082351 restraints weight = 158378.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.076847 restraints weight = 113532.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.074207 restraints weight = 123219.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.072623 restraints weight = 95214.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072585 restraints weight = 76712.012| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 27841 Z= 0.246 Angle : 0.794 21.983 38047 Z= 0.395 Chirality : 0.045 0.244 4347 Planarity : 0.005 0.136 4671 Dihedral : 12.341 131.984 4447 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.96 % Favored : 87.77 % Rotamer: Outliers : 3.61 % Allowed : 15.89 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.13), residues: 3298 helix: -0.84 (0.15), residues: 1116 sheet: -2.41 (0.25), residues: 372 loop : -3.33 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 560 TYR 0.031 0.002 TYR F 299 PHE 0.017 0.002 PHE B 15 TRP 0.015 0.002 TRP E 167 HIS 0.010 0.001 HIS K 264 Details of bonding type rmsd covalent geometry : bond 0.00546 (27791) covalent geometry : angle 0.75972 (38013) hydrogen bonds : bond 0.06507 ( 1010) hydrogen bonds : angle 6.21420 ( 2757) metal coordination : bond 0.02153 ( 50) metal coordination : angle 7.71415 ( 34) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 118 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8312 (mmm) cc_final: 0.8092 (tpp) REVERT: A 163 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8535 (p90) REVERT: A 402 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9114 (p) REVERT: A 626 MET cc_start: 0.8826 (ttm) cc_final: 0.8538 (ttm) REVERT: A 668 MET cc_start: 0.8989 (tmm) cc_final: 0.8360 (ttp) REVERT: A 899 MET cc_start: 0.8520 (mmm) cc_final: 0.7983 (mtp) REVERT: B 90 MET cc_start: 0.9521 (tmm) cc_final: 0.9297 (tmm) REVERT: D 67 MET cc_start: 0.8552 (ttt) cc_final: 0.8285 (tmm) REVERT: K 57 MET cc_start: 0.2818 (mmt) cc_final: 0.2205 (mpp) REVERT: K 195 MET cc_start: -0.0078 (mtt) cc_final: -0.0289 (mtt) REVERT: K 241 MET cc_start: -0.1408 (mtm) cc_final: -0.1667 (mpp) REVERT: F 235 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7789 (pp) REVERT: F 293 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6422 (mm) outliers start: 101 outliers final: 61 residues processed: 211 average time/residue: 0.1627 time to fit residues: 56.5790 Evaluate side-chains 173 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 108 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 500 MET Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 121 optimal weight: 0.0050 chunk 106 optimal weight: 0.0370 chunk 103 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 326 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 172 optimal weight: 0.5980 chunk 177 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 599 HIS ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS ** E 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.123883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.078401 restraints weight = 197291.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.070295 restraints weight = 131200.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.070061 restraints weight = 62999.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069325 restraints weight = 44107.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069447 restraints weight = 41237.413| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27841 Z= 0.131 Angle : 0.680 18.165 38047 Z= 0.342 Chirality : 0.042 0.231 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.969 129.210 4445 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.19 % Favored : 91.59 % Rotamer: Outliers : 2.53 % Allowed : 17.75 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.14), residues: 3298 helix: -0.25 (0.15), residues: 1122 sheet: -2.23 (0.24), residues: 412 loop : -3.01 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 75 TYR 0.024 0.001 TYR F 299 PHE 0.048 0.001 PHE B 15 TRP 0.015 0.001 TRP A 598 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00271 (27791) covalent geometry : angle 0.65359 (38013) hydrogen bonds : bond 0.05944 ( 1010) hydrogen bonds : angle 5.58116 ( 2757) metal coordination : bond 0.01812 ( 50) metal coordination : angle 6.29069 ( 34) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 126 time to evaluate : 0.989 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 454 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8821 (t0) REVERT: A 542 MET cc_start: 0.8389 (mmm) cc_final: 0.8099 (mmm) REVERT: A 668 MET cc_start: 0.8964 (tmm) cc_final: 0.8350 (ttp) REVERT: A 899 MET cc_start: 0.8487 (mmm) cc_final: 0.7936 (ttt) REVERT: B 90 MET cc_start: 0.9514 (tmm) cc_final: 0.9312 (tmm) REVERT: K 57 MET cc_start: 0.2779 (mmt) cc_final: 0.2244 (mpp) REVERT: K 72 MET cc_start: -0.4376 (ttm) cc_final: -0.4808 (ttm) REVERT: K 153 MET cc_start: 0.6712 (mmm) cc_final: 0.5095 (tpp) REVERT: K 195 MET cc_start: -0.0567 (mtt) cc_final: -0.0778 (mtt) REVERT: K 241 MET cc_start: -0.1164 (mtm) cc_final: -0.1563 (mpp) REVERT: E 429 MET cc_start: 0.8587 (mtp) cc_final: 0.7871 (mtp) REVERT: E 576 MET cc_start: 0.2180 (mtp) cc_final: 0.1728 (mtp) REVERT: F 235 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7293 (pp) REVERT: F 293 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6344 (mm) REVERT: F 429 MET cc_start: -0.0822 (OUTLIER) cc_final: -0.1082 (ttm) REVERT: F 562 ASN cc_start: 0.6204 (OUTLIER) cc_final: 0.5954 (p0) outliers start: 70 outliers final: 37 residues processed: 192 average time/residue: 0.1633 time to fit residues: 51.9897 Evaluate side-chains 152 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 323 optimal weight: 30.0000 chunk 202 optimal weight: 0.0770 chunk 291 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 301 optimal weight: 0.0980 chunk 279 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 216 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS B 104 ASN ** K 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 HIS ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS ** F 519 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 = 0.4335 r_free = 0.4335 target = 0.123140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075486 restraints weight = 160918.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.067508 restraints weight = 115295.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066601 restraints weight = 64917.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.065743 restraints weight = 44933.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.065613 restraints weight = 44637.169| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27841 Z= 0.147 Angle : 0.657 16.607 38047 Z= 0.330 Chirality : 0.042 0.243 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.776 130.656 4442 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.77 % Favored : 91.02 % Rotamer: Outliers : 3.05 % Allowed : 18.25 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.14), residues: 3298 helix: -0.00 (0.16), residues: 1122 sheet: -2.00 (0.26), residues: 369 loop : -2.82 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.020 0.001 TYR F 299 PHE 0.019 0.001 PHE B 15 TRP 0.011 0.001 TRP A 598 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00325 (27791) covalent geometry : angle 0.63421 (38013) hydrogen bonds : bond 0.05783 ( 1010) hydrogen bonds : angle 5.42992 ( 2757) metal coordination : bond 0.01505 ( 50) metal coordination : angle 5.82075 ( 34) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 121 time to evaluate : 0.718 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 668 MET cc_start: 0.8968 (tmm) cc_final: 0.8336 (ttp) REVERT: A 899 MET cc_start: 0.8478 (mmm) cc_final: 0.7962 (ttt) REVERT: K 57 MET cc_start: 0.2511 (mmt) cc_final: 0.2001 (mpp) REVERT: K 72 MET cc_start: -0.4138 (ttm) cc_final: -0.4722 (ttm) REVERT: K 195 MET cc_start: -0.0582 (mtt) cc_final: -0.0799 (mtt) REVERT: K 241 MET cc_start: -0.0980 (mtm) cc_final: -0.1203 (mpp) REVERT: E 429 MET cc_start: 0.8488 (mtp) cc_final: 0.7923 (mtp) REVERT: F 235 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7170 (pp) REVERT: F 293 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6370 (mm) REVERT: F 562 ASN cc_start: 0.6059 (OUTLIER) cc_final: 0.5828 (p0) outliers start: 85 outliers final: 50 residues processed: 197 average time/residue: 0.1551 time to fit residues: 51.4369 Evaluate side-chains 156 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 103 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 229 HIS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 129 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 410 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** 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 = 0.4344 r_free = 0.4344 target = 0.123469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.074056 restraints weight = 135173.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.069383 restraints weight = 100540.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.067866 restraints weight = 58655.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.066181 restraints weight = 45312.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065899 restraints weight = 38952.919| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27841 Z= 0.146 Angle : 0.652 15.567 38047 Z= 0.326 Chirality : 0.041 0.231 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.622 130.676 4440 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.35 % Favored : 91.44 % Rotamer: Outliers : 3.16 % Allowed : 18.42 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.14), residues: 3298 helix: 0.09 (0.16), residues: 1130 sheet: -1.89 (0.26), residues: 379 loop : -2.68 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 135 TYR 0.019 0.001 TYR E 582 PHE 0.036 0.001 PHE K 240 TRP 0.012 0.001 TRP A 598 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00318 (27791) covalent geometry : angle 0.62991 (38013) hydrogen bonds : bond 0.05693 ( 1010) hydrogen bonds : angle 5.26971 ( 2757) metal coordination : bond 0.01555 ( 50) metal coordination : angle 5.69173 ( 34) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 114 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.7661 (ttm) cc_final: 0.7400 (ttm) REVERT: A 668 MET cc_start: 0.8996 (tmm) cc_final: 0.8361 (ttp) REVERT: D 32 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7465 (pp20) REVERT: K 57 MET cc_start: 0.2616 (mmt) cc_final: 0.1967 (mpp) REVERT: K 195 MET cc_start: -0.0657 (mtt) cc_final: -0.0867 (mtt) REVERT: F 95 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8400 (p0) outliers start: 88 outliers final: 64 residues processed: 197 average time/residue: 0.1611 time to fit residues: 53.1782 Evaluate side-chains 171 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 105 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 229 HIS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 283 HIS Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 513 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 182 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 331 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 164 optimal weight: 40.0000 chunk 324 optimal weight: 30.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.123172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.075707 restraints weight = 179315.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070886 restraints weight = 113280.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070375 restraints weight = 66185.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070492 restraints weight = 45692.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070426 restraints weight = 53417.327| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27841 Z= 0.124 Angle : 0.631 14.179 38047 Z= 0.314 Chirality : 0.041 0.228 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.443 130.188 4438 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.77 % Favored : 92.02 % Rotamer: Outliers : 2.67 % Allowed : 19.30 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.14), residues: 3298 helix: 0.17 (0.15), residues: 1142 sheet: -1.68 (0.26), residues: 392 loop : -2.59 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 135 TYR 0.015 0.001 TYR F 476 PHE 0.013 0.001 PHE E 475 TRP 0.012 0.001 TRP A 598 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00268 (27791) covalent geometry : angle 0.61186 (38013) hydrogen bonds : bond 0.05596 ( 1010) hydrogen bonds : angle 5.06436 ( 2757) metal coordination : bond 0.01419 ( 50) metal coordination : angle 5.21748 ( 34) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 117 time to evaluate : 0.904 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 295 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.6065 (p90) REVERT: A 668 MET cc_start: 0.9034 (tmm) cc_final: 0.8432 (ttp) REVERT: A 899 MET cc_start: 0.8504 (tpp) cc_final: 0.7648 (ttt) REVERT: B 70 MET cc_start: 0.9286 (ttm) cc_final: 0.9050 (mmp) REVERT: D 32 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: D 55 MET cc_start: 0.8986 (tpp) cc_final: 0.8763 (tmm) REVERT: K 57 MET cc_start: 0.2896 (mmt) cc_final: 0.2404 (mpp) REVERT: E 233 MET cc_start: 0.8284 (ppp) cc_final: 0.8037 (ppp) REVERT: E 516 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.6525 (t0) REVERT: F 95 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8295 (p0) outliers start: 74 outliers final: 53 residues processed: 186 average time/residue: 0.1538 time to fit residues: 48.0969 Evaluate side-chains 161 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 104 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 229 HIS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 441 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 14 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 329 optimal weight: 30.0000 chunk 326 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 331 optimal weight: 5.9990 chunk 169 optimal weight: 0.4980 chunk 249 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 354 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 = 0.4329 r_free = 0.4329 target = 0.122922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.077388 restraints weight = 169090.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.071094 restraints weight = 135179.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.069694 restraints weight = 72403.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.069688 restraints weight = 47538.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070673 restraints weight = 46423.139| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27841 Z= 0.131 Angle : 0.634 13.892 38047 Z= 0.315 Chirality : 0.041 0.228 4347 Planarity : 0.004 0.058 4671 Dihedral : 11.348 130.697 4438 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.92 % Favored : 91.93 % Rotamer: Outliers : 2.56 % Allowed : 19.47 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3298 helix: 0.26 (0.16), residues: 1142 sheet: -1.60 (0.25), residues: 404 loop : -2.49 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 135 TYR 0.014 0.001 TYR A 217 PHE 0.013 0.001 PHE A 753 TRP 0.011 0.001 TRP A 598 HIS 0.010 0.001 HIS K 264 Details of bonding type rmsd covalent geometry : bond 0.00287 (27791) covalent geometry : angle 0.61266 (38013) hydrogen bonds : bond 0.05555 ( 1010) hydrogen bonds : angle 5.00065 ( 2757) metal coordination : bond 0.01536 ( 50) metal coordination : angle 5.49641 ( 34) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 111 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 MET cc_start: 0.8967 (tmm) cc_final: 0.8302 (ttp) REVERT: B 70 MET cc_start: 0.9245 (ttm) cc_final: 0.9037 (mmp) REVERT: B 94 MET cc_start: 0.9070 (ttp) cc_final: 0.8790 (ppp) REVERT: D 32 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: D 67 MET cc_start: 0.8549 (tmm) cc_final: 0.8056 (tmm) REVERT: K 57 MET cc_start: 0.2980 (mmt) cc_final: 0.2403 (mpp) REVERT: E 233 MET cc_start: 0.8393 (ppp) cc_final: 0.8138 (ppp) REVERT: E 429 MET cc_start: 0.8442 (mtp) cc_final: 0.7905 (mtp) REVERT: F 68 MET cc_start: 0.7536 (mmm) cc_final: 0.7332 (tpp) REVERT: F 95 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8421 (p0) outliers start: 71 outliers final: 58 residues processed: 177 average time/residue: 0.1541 time to fit residues: 45.3176 Evaluate side-chains 166 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 106 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 229 HIS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 513 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 56 optimal weight: 0.9990 chunk 303 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 179 optimal weight: 30.0000 chunk 20 optimal weight: 0.4980 chunk 297 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN F 268 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.122591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.067423 restraints weight = 156910.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.064942 restraints weight = 79945.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063994 restraints weight = 69020.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.063574 restraints weight = 51511.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.063471 restraints weight = 48375.417| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27841 Z= 0.163 Angle : 0.662 14.187 38047 Z= 0.326 Chirality : 0.041 0.230 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.283 131.410 4438 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.38 % Favored : 91.44 % Rotamer: Outliers : 2.63 % Allowed : 19.68 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.14), residues: 3298 helix: 0.24 (0.16), residues: 1137 sheet: -1.60 (0.26), residues: 383 loop : -2.45 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.019 0.001 TYR A 217 PHE 0.020 0.001 PHE K 240 TRP 0.021 0.001 TRP K 186 HIS 0.007 0.001 HIS K 19 Details of bonding type rmsd covalent geometry : bond 0.00361 (27791) covalent geometry : angle 0.63855 (38013) hydrogen bonds : bond 0.05575 ( 1010) hydrogen bonds : angle 5.05399 ( 2757) metal coordination : bond 0.01580 ( 50) metal coordination : angle 5.91224 ( 34) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 108 time to evaluate : 0.943 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 668 MET cc_start: 0.9041 (tmm) cc_final: 0.8308 (ttp) REVERT: A 899 MET cc_start: 0.8278 (tpp) cc_final: 0.7726 (ttt) REVERT: B 94 MET cc_start: 0.9155 (ttp) cc_final: 0.8876 (ppp) REVERT: D 32 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7599 (pp20) REVERT: K 57 MET cc_start: 0.2655 (mmt) cc_final: 0.1960 (mpp) REVERT: E 516 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7727 (t0) REVERT: F 95 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8311 (p0) outliers start: 73 outliers final: 62 residues processed: 177 average time/residue: 0.1529 time to fit residues: 45.3850 Evaluate side-chains 170 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 105 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 229 HIS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 513 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 306 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 135 optimal weight: 0.0010 chunk 249 optimal weight: 0.5980 chunk 317 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 354 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 = 0.4348 r_free = 0.4348 target = 0.123738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.077426 restraints weight = 154931.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071466 restraints weight = 126135.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.069938 restraints weight = 70251.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.067144 restraints weight = 47774.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067011 restraints weight = 36571.654| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27841 Z= 0.132 Angle : 0.653 13.907 38047 Z= 0.320 Chirality : 0.041 0.228 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.199 130.866 4438 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.17 % Rotamer: Outliers : 2.42 % Allowed : 19.93 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.14), residues: 3298 helix: 0.28 (0.16), residues: 1145 sheet: -1.44 (0.26), residues: 376 loop : -2.39 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 135 TYR 0.014 0.001 TYR A 217 PHE 0.013 0.001 PHE A 753 TRP 0.016 0.001 TRP K 186 HIS 0.007 0.001 HIS K 19 Details of bonding type rmsd covalent geometry : bond 0.00291 (27791) covalent geometry : angle 0.63120 (38013) hydrogen bonds : bond 0.05534 ( 1010) hydrogen bonds : angle 4.95380 ( 2757) metal coordination : bond 0.01654 ( 50) metal coordination : angle 5.58431 ( 34) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 113 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 MET cc_start: 0.8991 (tmm) cc_final: 0.8324 (ttp) REVERT: A 899 MET cc_start: 0.8431 (tpp) cc_final: 0.7880 (ttt) REVERT: D 32 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: K 57 MET cc_start: 0.3157 (mmt) cc_final: 0.2384 (mpp) REVERT: E 516 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.6523 (t0) REVERT: F 95 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8167 (p0) outliers start: 67 outliers final: 60 residues processed: 176 average time/residue: 0.1550 time to fit residues: 45.8608 Evaluate side-chains 172 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 109 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 229 HIS Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 283 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 513 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 148 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 306 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 33 optimal weight: 0.0570 chunk 291 optimal weight: 10.0000 chunk 268 optimal weight: 0.1980 chunk 261 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 overall best weight: 3.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 354 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 = 0.4302 r_free = 0.4302 target = 0.122157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066084 restraints weight = 173659.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.066565 restraints weight = 95484.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.063350 restraints weight = 67487.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.062623 restraints weight = 53245.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.062153 restraints weight = 44537.109| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27841 Z= 0.207 Angle : 0.697 15.644 38047 Z= 0.342 Chirality : 0.042 0.231 4347 Planarity : 0.004 0.056 4671 Dihedral : 11.204 132.630 4436 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.98 % Favored : 90.83 % Rotamer: Outliers : 2.39 % Allowed : 19.89 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3298 helix: 0.13 (0.15), residues: 1143 sheet: -1.48 (0.27), residues: 376 loop : -2.41 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 135 TYR 0.022 0.001 TYR A 217 PHE 0.016 0.001 PHE A 753 TRP 0.021 0.001 TRP K 186 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00462 (27791) covalent geometry : angle 0.67350 (38013) hydrogen bonds : bond 0.05676 ( 1010) hydrogen bonds : angle 5.14745 ( 2757) metal coordination : bond 0.01667 ( 50) metal coordination : angle 6.05742 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10939.96 seconds wall clock time: 186 minutes 38.75 seconds (11198.75 seconds total)