Starting phenix.real_space_refine on Sun Jul 5 23:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eiz_31146/07_2026/7eiz_31146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eiz_31146/07_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_31146/07_2026/7eiz_31146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eiz_31146/07_2026/7eiz_31146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eiz_31146/07_2026/7eiz_31146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eiz_31146/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 6.60, per 1000 atoms: 0.24 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 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: 3.42 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: 5.36 Time building geometry restraints manager: 3.41 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=" N9 A I 32 " pdb=" C4 A I 32 " ideal model delta sigma weight residual 1.374 1.328 0.046 6.00e-03 2.78e+04 5.93e+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=" N3 A I 29 " pdb=" C4 A I 29 " ideal model delta sigma weight residual 1.344 1.309 0.035 6.00e-03 2.78e+04 3.40e+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=" N1 C J 34 " pdb=" C2 C J 34 " pdb=" O2 C J 34 " ideal model delta sigma weight residual 118.90 115.06 3.84 6.00e-01 2.78e+00 4.09e+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 ... (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: 3.760 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 32.070 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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= 0.671 Angle : 1.243 42.836 38047 Z= 0.702 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/Z covalent geometry : bond 0.01283 / 0.66 (27791) covalent geometry : angle 1.17074 / 0.70 (38013) hydrogen bonds : bond 0.19435 / 13.01 ( 1010) hydrogen bonds : angle 9.22828 / 6.24 ( 2757) metal coordination : bond 0.10909 / 6.72 ( 50) metal coordination : angle 13.97772 / 10.23 ( 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 : 1.042 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: 0.2106 time to fit residues: 54.9345 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 : 1.062 ------------------------------------------------------------------------------- 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... ** 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 611 ASN A 815 GLN B 65 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN G 1 ASN G 11 GLN H 65 GLN K 22 GLN K 104 ASN E 268 ASN E 361 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.123556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.077551 restraints weight = 168743.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.069842 restraints weight = 132518.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.069144 restraints weight = 101896.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.070283 restraints weight = 86181.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.069767 restraints weight = 74592.988| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 27841 Z= 0.238 Angle : 0.887 25.457 38047 Z= 0.450 Chirality : 0.048 0.294 4347 Planarity : 0.006 0.140 4671 Dihedral : 12.857 125.601 4451 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.44 % Favored : 87.25 % Rotamer: Outliers : 2.74 % Allowed : 14.88 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -4.18 (0.12), residues: 3298 helix: -1.74 (0.14), residues: 1126 sheet: -2.75 (0.23), residues: 406 loop : -3.62 (0.12), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 560 TYR 0.030 0.002 TYR F 299 PHE 0.021 0.002 PHE B 15 TRP 0.023 0.002 TRP E 167 HIS 0.019 0.002 HIS K 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 (27791) covalent geometry : angle 0.84128 / 0.45 (38013) hydrogen bonds : bond 0.07509 / 4.92 ( 1010) hydrogen bonds : angle 6.81510 / 4.65 ( 2757) metal coordination : bond 0.03176 / 1.63 ( 50) metal coordination : angle 9.47998 / 6.75 ( 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: 76 poor density : 128 time to evaluate : 1.038 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 110 MET cc_start: 0.8460 (mmm) cc_final: 0.7926 (tpp) REVERT: A 454 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8825 (t0) REVERT: A 668 MET cc_start: 0.8876 (tmm) cc_final: 0.8384 (ttp) REVERT: A 906 MET cc_start: 0.7963 (tmm) cc_final: 0.7710 (tmm) REVERT: B 62 MET cc_start: 0.8623 (ppp) cc_final: 0.8153 (ppp) REVERT: B 90 MET cc_start: 0.9421 (tmm) cc_final: 0.9025 (tmm) REVERT: B 174 MET cc_start: 0.8668 (tpt) cc_final: 0.8426 (tpp) REVERT: C 28 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9232 (mt) REVERT: K 57 MET cc_start: 0.2780 (mmt) cc_final: 0.2048 (mpp) REVERT: K 153 MET cc_start: 0.6716 (mmm) cc_final: 0.6364 (mmm) REVERT: E 233 MET cc_start: 0.8579 (mmt) cc_final: 0.8319 (ppp) REVERT: E 436 MET cc_start: 0.7926 (mpp) cc_final: 0.7705 (mpp) outliers start: 76 outliers final: 37 residues processed: 197 average time/residue: 0.1817 time to fit residues: 58.3466 Evaluate side-chains 143 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 331 ARG 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 454 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 VAL 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 28 LEU 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 128 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 149 LEU 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 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: 4.9990 chunk 252 optimal weight: 0.9990 chunk 232 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 chunk 231 optimal weight: 30.0000 chunk 239 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 270 optimal weight: 0.5980 chunk 199 optimal weight: 40.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 A 599 HIS ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 116 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.124077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.074924 restraints weight = 157437.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.068266 restraints weight = 127110.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065472 restraints weight = 100593.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.062229 restraints weight = 76317.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.062253 restraints weight = 67399.175| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 27841 Z= 0.187 Angle : 0.765 22.355 38047 Z= 0.387 Chirality : 0.045 0.251 4347 Planarity : 0.005 0.134 4671 Dihedral : 12.461 128.507 4447 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.59 % Favored : 88.13 % Rotamer: Outliers : 3.05 % Allowed : 16.32 % Favored : 80.63 % 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: -3.41 (0.13), residues: 3298 helix: -0.89 (0.15), residues: 1116 sheet: -2.33 (0.25), residues: 371 loop : -3.30 (0.13), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 560 TYR 0.032 0.002 TYR F 299 PHE 0.018 0.002 PHE B 15 TRP 0.014 0.002 TRP A 598 HIS 0.009 0.001 HIS K 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (27791) covalent geometry : angle 0.72824 / 0.38 (38013) hydrogen bonds : bond 0.06742 / 4.45 ( 1010) hydrogen bonds : angle 6.24454 / 4.29 ( 2757) metal coordination : bond 0.02366 / 1.17 ( 50) metal coordination : angle 7.91087 / 5.51 ( 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 200 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 115 time to evaluate : 1.083 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 110 MET cc_start: 0.8580 (mmm) cc_final: 0.8206 (tpp) REVERT: A 542 MET cc_start: 0.8331 (mmm) cc_final: 0.8078 (mmm) REVERT: A 668 MET cc_start: 0.8958 (tmm) cc_final: 0.8313 (ttp) REVERT: B 90 MET cc_start: 0.9470 (tmm) cc_final: 0.9158 (tmm) REVERT: K 57 MET cc_start: 0.2366 (mmt) cc_final: 0.1719 (mpp) REVERT: K 62 MET cc_start: 0.1149 (tmm) cc_final: 0.0787 (tmm) REVERT: K 72 MET cc_start: -0.4132 (ttm) cc_final: -0.4348 (ttm) REVERT: K 501 MET cc_start: -0.3169 (tpp) cc_final: -0.3453 (tpp) REVERT: E 233 MET cc_start: 0.8579 (mmt) cc_final: 0.8282 (ppp) REVERT: E 429 MET cc_start: 0.8258 (mtp) cc_final: 0.7772 (mtp) REVERT: F 293 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5797 (mm) outliers start: 85 outliers final: 50 residues processed: 194 average time/residue: 0.1766 time to fit residues: 56.5599 Evaluate side-chains 158 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 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 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 393 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 VAL 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 898 HIS 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 B residue 94 MET Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 SER 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 182 TRP Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 120 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 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 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 159 SER 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: 0.0040 chunk 106 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 202 optimal weight: 30.0000 chunk 125 optimal weight: 0.6980 chunk 326 optimal weight: 20.0000 chunk 26 optimal weight: 0.3980 chunk 291 optimal weight: 20.0000 chunk 172 optimal weight: 0.0970 chunk 177 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.123207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.083085 restraints weight = 199476.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076286 restraints weight = 143317.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076609 restraints weight = 77320.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.075565 restraints weight = 46658.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.075032 restraints weight = 44764.516| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 27841 Z= 0.138 Angle : 0.695 18.578 38047 Z= 0.353 Chirality : 0.043 0.228 4347 Planarity : 0.004 0.055 4671 Dihedral : 12.062 128.384 4445 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.47 % Favored : 91.29 % Rotamer: Outliers : 2.63 % Allowed : 17.33 % Favored : 80.04 % 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: -2.86 (0.14), residues: 3298 helix: -0.34 (0.15), residues: 1123 sheet: -2.13 (0.25), residues: 383 loop : -3.02 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 476 TYR 0.026 0.001 TYR F 299 PHE 0.042 0.002 PHE B 15 TRP 0.013 0.001 TRP A 598 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (27791) covalent geometry : angle 0.66815 / 0.35 (38013) hydrogen bonds : bond 0.06197 / 4.16 ( 1010) hydrogen bonds : angle 5.65633 / 3.93 ( 2757) metal coordination : bond 0.01996 / 1.05 ( 50) metal coordination : angle 6.41716 / 4.37 ( 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: 73 poor density : 123 time to evaluate : 1.035 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 331 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8325 (ttp80) REVERT: A 454 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8847 (t0) REVERT: A 668 MET cc_start: 0.9001 (tmm) cc_final: 0.8374 (ttp) REVERT: B 49 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8700 (m-10) REVERT: B 90 MET cc_start: 0.9465 (tmm) cc_final: 0.9214 (tmm) REVERT: D 129 MET cc_start: 0.7774 (mmm) cc_final: 0.7383 (mmm) REVERT: K 57 MET cc_start: 0.3016 (mmt) cc_final: 0.2649 (mpp) REVERT: K 153 MET cc_start: 0.5919 (mmm) cc_final: 0.5644 (tpt) REVERT: K 241 MET cc_start: -0.2105 (mpp) cc_final: -0.2473 (mpp) REVERT: K 501 MET cc_start: -0.1697 (tpp) cc_final: -0.2071 (tpp) REVERT: E 576 MET cc_start: 0.2339 (mtp) cc_final: 0.1762 (mtm) REVERT: F 293 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6385 (mm) REVERT: F 429 MET cc_start: -0.1348 (OUTLIER) cc_final: -0.1570 (ttm) outliers start: 73 outliers final: 33 residues processed: 190 average time/residue: 0.1732 time to fit residues: 54.0629 Evaluate side-chains 144 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 454 ASP 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 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 76 VAL 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 374 ASP 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 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 513 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 323 optimal weight: 5.9990 chunk 202 optimal weight: 50.0000 chunk 291 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 173 optimal weight: 50.0000 chunk 301 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 216 optimal weight: 0.0870 chunk 18 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 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** D 108 ASN G 98 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** 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 116 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.122122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.067073 restraints weight = 158277.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.061491 restraints weight = 85492.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.060031 restraints weight = 47143.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060098 restraints weight = 46573.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060098 restraints weight = 43258.583| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 27841 Z= 0.214 Angle : 0.711 17.941 38047 Z= 0.358 Chirality : 0.043 0.233 4347 Planarity : 0.004 0.055 4671 Dihedral : 11.945 131.164 4442 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.92 % Favored : 89.80 % Rotamer: Outliers : 3.05 % Allowed : 18.28 % Favored : 78.67 % 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: -2.77 (0.14), residues: 3298 helix: -0.27 (0.15), residues: 1131 sheet: -2.07 (0.25), residues: 379 loop : -2.97 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 579 TYR 0.024 0.002 TYR F 299 PHE 0.035 0.002 PHE B 15 TRP 0.011 0.001 TRP A 598 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (27791) covalent geometry : angle 0.68437 / 0.36 (38013) hydrogen bonds : bond 0.06152 / 4.12 ( 1010) hydrogen bonds : angle 5.73378 / 3.96 ( 2757) metal coordination : bond 0.01596 / 0.81 ( 50) metal coordination : angle 6.45653 / 4.40 ( 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 202 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 117 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8357 (ttp80) REVERT: A 542 MET cc_start: 0.8481 (mmm) cc_final: 0.8046 (mmm) REVERT: A 668 MET cc_start: 0.9043 (tmm) cc_final: 0.8412 (ttp) REVERT: B 90 MET cc_start: 0.9500 (tmm) cc_final: 0.9180 (tmm) REVERT: D 129 MET cc_start: 0.7909 (mmm) cc_final: 0.7463 (mmm) REVERT: H 44 MET cc_start: 0.4438 (tpt) cc_final: 0.3864 (tpt) REVERT: K 41 ASP cc_start: 0.5869 (p0) cc_final: 0.5644 (m-30) REVERT: K 57 MET cc_start: 0.2663 (mmt) cc_final: 0.2133 (mpp) REVERT: K 72 MET cc_start: -0.3658 (ttm) cc_final: -0.4180 (ttm) REVERT: K 153 MET cc_start: 0.6344 (mmm) cc_final: 0.6122 (tpt) REVERT: E 429 MET cc_start: 0.7317 (mtp) cc_final: 0.7010 (ttt) REVERT: F 189 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8217 (tmtt) REVERT: F 293 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5651 (mm) outliers start: 85 outliers final: 61 residues processed: 193 average time/residue: 0.1731 time to fit residues: 55.5449 Evaluate side-chains 167 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 104 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 141 THR 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 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 ARG 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 544 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU 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 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 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 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 G residue 76 VAL Chi-restraints excluded: chain K residue 74 ILE 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 120 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 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 592 ILE Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 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 513 SER Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 129 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 174 optimal weight: 0.1980 chunk 206 optimal weight: 0.0040 chunk 79 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 HIS F 88 GLN F 281 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.123599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.078843 restraints weight = 140086.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.070173 restraints weight = 108366.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.068955 restraints weight = 58451.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.070662 restraints weight = 45574.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.069016 restraints weight = 36096.700| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27841 Z= 0.128 Angle : 0.660 17.262 38047 Z= 0.332 Chirality : 0.042 0.231 4347 Planarity : 0.004 0.056 4671 Dihedral : 11.847 130.350 4442 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.10 % Favored : 91.68 % Rotamer: Outliers : 2.88 % Allowed : 18.98 % Favored : 78.14 % 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: -0.01 (0.15), residues: 1121 sheet: -1.87 (0.26), residues: 386 loop : -2.84 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 76 TYR 0.021 0.001 TYR F 299 PHE 0.029 0.001 PHE B 15 TRP 0.013 0.001 TRP A 598 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (27791) covalent geometry : angle 0.63724 / 0.33 (38013) hydrogen bonds : bond 0.06017 / 4.07 ( 1010) hydrogen bonds : angle 5.40207 / 3.75 ( 2757) metal coordination : bond 0.01689 / 0.91 ( 50) metal coordination : angle 5.79806 / 3.92 ( 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 200 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 120 time to evaluate : 1.068 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 331 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8220 (ttp80) REVERT: A 454 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8830 (t0) REVERT: A 542 MET cc_start: 0.8326 (mmm) cc_final: 0.7986 (mmm) REVERT: A 668 MET cc_start: 0.8959 (tmm) cc_final: 0.8338 (ttp) REVERT: B 90 MET cc_start: 0.9466 (tmm) cc_final: 0.9215 (tmm) REVERT: D 129 MET cc_start: 0.7714 (mmm) cc_final: 0.7304 (mmm) REVERT: K 57 MET cc_start: 0.2706 (mmt) cc_final: 0.2175 (mpp) REVERT: K 153 MET cc_start: 0.6200 (mmm) cc_final: 0.5966 (tpt) REVERT: E 429 MET cc_start: 0.8388 (mtp) cc_final: 0.7826 (mtp) REVERT: F 116 ASN cc_start: 0.9401 (OUTLIER) cc_final: 0.9116 (p0) REVERT: F 293 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6330 (mm) outliers start: 80 outliers final: 47 residues processed: 196 average time/residue: 0.1763 time to fit residues: 56.8631 Evaluate side-chains 159 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 331 ARG 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 454 ASP 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 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 46 LYS 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 182 TRP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 120 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 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 592 ILE Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 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 513 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 182 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 324 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN A 928 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 410 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.122524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.071867 restraints weight = 170343.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064825 restraints weight = 109895.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.065281 restraints weight = 61095.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.063162 restraints weight = 42131.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.063440 restraints weight = 40597.438| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 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 = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27841 Z= 0.208 Angle : 0.696 16.826 38047 Z= 0.350 Chirality : 0.043 0.234 4347 Planarity : 0.004 0.056 4671 Dihedral : 11.751 131.681 4440 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.47 % Favored : 90.32 % Rotamer: Outliers : 3.26 % Allowed : 19.02 % 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: -2.51 (0.14), residues: 3298 helix: -0.14 (0.15), residues: 1135 sheet: -1.88 (0.26), residues: 373 loop : -2.76 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 392 TYR 0.023 0.001 TYR A 217 PHE 0.025 0.002 PHE B 15 TRP 0.011 0.001 TRP A 598 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (27791) covalent geometry : angle 0.67278 / 0.35 (38013) hydrogen bonds : bond 0.06048 / 4.08 ( 1010) hydrogen bonds : angle 5.52087 / 3.82 ( 2757) metal coordination : bond 0.01408 / 0.73 ( 50) metal coordination : angle 5.96339 / 4.03 ( 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 205 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 114 time to evaluate : 1.070 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 19 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8695 (tp) REVERT: A 454 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8945 (t0) REVERT: A 542 MET cc_start: 0.8518 (mmm) cc_final: 0.8119 (mmm) REVERT: A 668 MET cc_start: 0.9052 (tmm) cc_final: 0.8383 (ttp) REVERT: B 90 MET cc_start: 0.9494 (tmm) cc_final: 0.9223 (tmm) REVERT: D 55 MET cc_start: 0.9078 (tpp) cc_final: 0.8861 (tmm) REVERT: D 129 MET cc_start: 0.7808 (mmm) cc_final: 0.7466 (mmm) REVERT: K 57 MET cc_start: 0.2637 (mmt) cc_final: 0.2119 (mpp) REVERT: K 153 MET cc_start: 0.6353 (mmm) cc_final: 0.6142 (tpt) REVERT: E 429 MET cc_start: 0.8299 (mtp) cc_final: 0.7781 (ttp) REVERT: F 293 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.6147 (mm) outliers start: 91 outliers final: 70 residues processed: 198 average time/residue: 0.1736 time to fit residues: 57.1859 Evaluate side-chains 177 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 104 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 141 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 293 THR 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 454 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU 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 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 84 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 57 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 G residue 76 VAL Chi-restraints excluded: chain G residue 97 LEU 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 120 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 K residue 283 HIS 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 477 LYS Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 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 513 SER Chi-restraints excluded: chain F residue 576 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 14 optimal weight: 0.3980 chunk 244 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 326 optimal weight: 30.0000 chunk 283 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS C 19 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** 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 ** 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 = 0.4328 r_free = 0.4328 target = 0.122927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.068155 restraints weight = 158782.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.065056 restraints weight = 87132.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.064273 restraints weight = 63150.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.064376 restraints weight = 49866.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.063662 restraints weight = 53178.507| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27841 Z= 0.173 Angle : 0.673 17.084 38047 Z= 0.338 Chirality : 0.042 0.279 4347 Planarity : 0.004 0.056 4671 Dihedral : 11.628 131.563 4438 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.92 % Favored : 90.86 % Rotamer: Outliers : 3.02 % Allowed : 19.30 % 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: -2.40 (0.14), residues: 3298 helix: -0.03 (0.15), residues: 1130 sheet: -1.80 (0.26), residues: 379 loop : -2.71 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.018 0.001 TYR A 149 PHE 0.023 0.001 PHE B 15 TRP 0.012 0.001 TRP A 598 HIS 0.009 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (27791) covalent geometry : angle 0.64834 / 0.34 (38013) hydrogen bonds : bond 0.05973 / 4.06 ( 1010) hydrogen bonds : angle 5.40102 / 3.74 ( 2757) metal coordination : bond 0.01550 / 0.84 ( 50) metal coordination : angle 6.12607 / 4.22 ( 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 192 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 108 time to evaluate : 1.060 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 331 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8331 (ttp80) REVERT: A 454 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8951 (t0) REVERT: A 542 MET cc_start: 0.8519 (mmm) cc_final: 0.8130 (mmm) REVERT: A 668 MET cc_start: 0.9070 (tmm) cc_final: 0.8377 (ttp) REVERT: B 90 MET cc_start: 0.9519 (tmm) cc_final: 0.9254 (tmm) REVERT: D 55 MET cc_start: 0.9211 (tpp) cc_final: 0.8922 (tmm) REVERT: D 129 MET cc_start: 0.7869 (mmm) cc_final: 0.7429 (mmm) REVERT: K 57 MET cc_start: 0.2507 (mmt) cc_final: 0.1789 (mpp) REVERT: K 72 MET cc_start: -0.2841 (ttm) cc_final: -0.3408 (ttt) REVERT: E 576 MET cc_start: -0.1088 (ptp) cc_final: -0.1364 (ptt) REVERT: F 293 ILE cc_start: 0.6093 (OUTLIER) cc_final: 0.5844 (mm) outliers start: 84 outliers final: 63 residues processed: 185 average time/residue: 0.1748 time to fit residues: 53.6695 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 : 1.005 ------------------------------------------------------------------------------- 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 293 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 ARG 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 454 ASP Chi-restraints excluded: chain A residue 544 LEU 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 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 B residue 84 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 51 LYS 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 G residue 97 LEU Chi-restraints excluded: chain H residue 14 LEU 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 120 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 272 CYS Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 266 VAL 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 592 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 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 513 SER Chi-restraints excluded: chain F residue 576 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 56 optimal weight: 5.9990 chunk 303 optimal weight: 40.0000 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 179 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 297 optimal weight: 0.0030 chunk 208 optimal weight: 0.0040 chunk 241 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 210 GLN ** 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** C 19 GLN ** D 157 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 88 GLN ** 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 = 0.4328 r_free = 0.4328 target = 0.123278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.076249 restraints weight = 162155.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071256 restraints weight = 119658.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.068397 restraints weight = 70432.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.068314 restraints weight = 49258.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.068177 restraints weight = 46801.750| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27841 Z= 0.127 Angle : 0.650 15.267 38047 Z= 0.325 Chirality : 0.041 0.264 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.445 130.437 4438 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.47 % Favored : 91.32 % Rotamer: Outliers : 2.21 % Allowed : 20.14 % 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: -2.25 (0.14), residues: 3298 helix: 0.11 (0.15), residues: 1131 sheet: -1.71 (0.26), residues: 394 loop : -2.64 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.015 0.001 TYR F 299 PHE 0.021 0.001 PHE B 15 TRP 0.014 0.001 TRP A 598 HIS 0.008 0.001 HIS K 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (27791) covalent geometry : angle 0.62598 / 0.32 (38013) hydrogen bonds : bond 0.05899 / 4.03 ( 1010) hydrogen bonds : angle 5.17788 / 3.60 ( 2757) metal coordination : bond 0.01706 / 1.01 ( 50) metal coordination : angle 5.89898 / 4.03 ( 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 176 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 115 time to evaluate : 0.906 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 331 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8243 (ttp80) REVERT: A 454 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8881 (t0) REVERT: A 542 MET cc_start: 0.8409 (mmm) cc_final: 0.8029 (mmm) REVERT: A 668 MET cc_start: 0.9018 (tmm) cc_final: 0.8341 (ttp) REVERT: B 90 MET cc_start: 0.9441 (tmm) cc_final: 0.9240 (tmm) REVERT: K 57 MET cc_start: 0.2642 (mmt) cc_final: 0.1926 (mpp) REVERT: K 72 MET cc_start: -0.2914 (ttm) cc_final: -0.3275 (ttt) outliers start: 61 outliers final: 48 residues processed: 168 average time/residue: 0.1776 time to fit residues: 49.3100 Evaluate side-chains 156 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 331 ARG Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 454 ASP 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 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 51 LYS 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 G residue 97 LEU Chi-restraints excluded: chain H residue 14 LEU 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 120 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 242 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 592 ILE 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 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 Chi-restraints excluded: chain F residue 576 MET 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: 40.0000 chunk 85 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 317 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 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** F 11 GLN F 88 GLN F 268 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.123279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.073084 restraints weight = 153626.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.068678 restraints weight = 110870.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066355 restraints weight = 72612.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065918 restraints weight = 52738.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.065613 restraints weight = 52160.723| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27841 Z= 0.163 Angle : 0.677 15.317 38047 Z= 0.336 Chirality : 0.042 0.274 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.370 131.467 4438 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.41 % Favored : 91.38 % Rotamer: Outliers : 2.28 % Allowed : 20.25 % Favored : 77.47 % 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: -2.21 (0.14), residues: 3298 helix: 0.09 (0.15), residues: 1131 sheet: -1.70 (0.27), residues: 376 loop : -2.56 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 99 TYR 0.017 0.001 TYR A 217 PHE 0.021 0.001 PHE B 15 TRP 0.018 0.001 TRP E 167 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (27791) covalent geometry : angle 0.65078 / 0.33 (38013) hydrogen bonds : bond 0.05867 / 3.99 ( 1010) hydrogen bonds : angle 5.23351 / 3.64 ( 2757) metal coordination : bond 0.01588 / 0.90 ( 50) metal coordination : angle 6.23124 / 4.23 ( 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 169 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 106 time to evaluate : 1.012 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 242 MET cc_start: 0.8959 (mmm) cc_final: 0.8639 (mmm) REVERT: A 331 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8251 (ttp80) REVERT: A 454 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8916 (t0) REVERT: A 542 MET cc_start: 0.8479 (mmm) cc_final: 0.8085 (mmm) REVERT: A 668 MET cc_start: 0.9016 (tmm) cc_final: 0.8350 (ttp) REVERT: B 90 MET cc_start: 0.9403 (tmm) cc_final: 0.9195 (tmm) REVERT: K 57 MET cc_start: 0.2523 (mmt) cc_final: 0.1785 (mpp) REVERT: F 11 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8261 (mp10) outliers start: 63 outliers final: 56 residues processed: 164 average time/residue: 0.1716 time to fit residues: 46.4563 Evaluate side-chains 164 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 105 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 293 THR Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 454 ASP 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 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 49 PHE Chi-restraints excluded: chain B residue 94 MET 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 G residue 97 LEU Chi-restraints excluded: chain H residue 14 LEU 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 120 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 242 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 266 VAL 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 592 ILE Chi-restraints excluded: chain F residue 11 GLN 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 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 Chi-restraints excluded: chain F residue 576 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 148 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 306 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 291 optimal weight: 20.0000 chunk 268 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN F 268 ASN ** 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 = 0.4340 r_free = 0.4340 target = 0.123169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.067042 restraints weight = 163776.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.068090 restraints weight = 84420.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.066742 restraints weight = 54740.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.065392 restraints weight = 43087.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.064483 restraints weight = 42472.837| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.396 27841 Z= 0.206 Angle : 0.784 59.199 38047 Z= 0.413 Chirality : 0.042 0.485 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.370 131.460 4438 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.41 % Favored : 91.38 % Rotamer: Outliers : 2.35 % Allowed : 20.18 % Favored : 77.47 % Cbeta Deviations : 0.03 % 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: -2.22 (0.14), residues: 3298 helix: 0.09 (0.15), residues: 1131 sheet: -1.70 (0.27), residues: 376 loop : -2.57 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.024 0.001 TYR F 476 PHE 0.020 0.001 PHE B 15 TRP 0.110 0.002 TRP K 186 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (27791) covalent geometry : angle 0.76173 / 0.41 (38013) hydrogen bonds : bond 0.05878 / 4.00 ( 1010) hydrogen bonds : angle 5.23574 / 3.64 ( 2757) metal coordination : bond 0.01587 / 0.90 ( 50) metal coordination : angle 6.21754 / 4.22 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12651.55 seconds wall clock time: 216 minutes 5.84 seconds (12965.84 seconds total)