Starting phenix.real_space_refine on Mon Sep 14 14:40:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eiz_31146/09_2026/7eiz_31146.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eiz_31146/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7eiz_31146/09_2026/7eiz_31146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eiz_31146/09_2026/7eiz_31146.map" model { file = "/net/cci-nas-00/data/ceres_data/7eiz_31146/09_2026/7eiz_31146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eiz_31146/09_2026/7eiz_31146.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4911 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 13 6.06 5 P 52 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 17003 2.51 5 N 4589 2.21 5 O 5217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 7.00, per 1000 atoms: 0.26 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: 2.62 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: 3.11 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: 5.51 Time building geometry restraints manager: 3.40 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: 37433 3.67 - 7.33: 527 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: 2982 0.054 - 0.107: 1067 0.107 - 0.161: 263 0.161 - 0.214: 29 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 32.580 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- 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= 0.678 Angle : 1.252 42.836 38047 Z= 0.710 Chirality : 0.057 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 0.01284 / 0.67 (27791) covalent geometry : angle 1.18118 / 0.71 (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 : 1.084 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: 0.2097 time to fit residues: 54.9531 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 : 1.054 ------------------------------------------------------------------------------- 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 815 GLN B 65 GLN B 118 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN G 11 GLN H 65 GLN K 22 GLN K 104 ASN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN E 361 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 GLN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.123608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.079387 restraints weight = 167954.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.070920 restraints weight = 133259.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068776 restraints weight = 106037.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067434 restraints weight = 77067.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.067268 restraints weight = 62655.479| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 27841 Z= 0.229 Angle : 0.901 27.493 38047 Z= 0.453 Chirality : 0.048 0.308 4347 Planarity : 0.006 0.140 4671 Dihedral : 12.912 128.025 4451 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.75 % Favored : 86.92 % Rotamer: Outliers : 2.70 % Allowed : 14.95 % Favored : 82.35 % 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: -4.25 (0.12), residues: 3298 helix: -1.81 (0.14), residues: 1115 sheet: -2.76 (0.22), residues: 414 loop : -3.65 (0.12), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 560 TYR 0.029 0.002 TYR F 299 PHE 0.021 0.002 PHE B 15 TRP 0.021 0.002 TRP E 167 HIS 0.016 0.002 HIS K 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (27791) covalent geometry : angle 0.84953 / 0.45 (38013) hydrogen bonds : bond 0.07748 / 5.05 ( 1010) hydrogen bonds : angle 6.88045 / 4.70 ( 2757) metal coordination : bond 0.03265 / 1.68 ( 50) metal coordination : angle 10.12332 / 7.23 ( 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 197 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 122 time to evaluate : 1.055 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: 0.8203 (mmm) cc_final: 0.7571 (tpp) REVERT: A 126 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 454 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8862 (t0) REVERT: A 668 MET cc_start: 0.8909 (tmm) cc_final: 0.8396 (ttp) REVERT: A 906 MET cc_start: 0.7838 (tmm) cc_final: 0.7602 (tmm) REVERT: B 62 MET cc_start: 0.8611 (ppp) cc_final: 0.8128 (ppp) REVERT: B 90 MET cc_start: 0.9431 (tmm) cc_final: 0.9089 (tmm) REVERT: B 174 MET cc_start: 0.8650 (tpt) cc_final: 0.8411 (tpp) REVERT: K 57 MET cc_start: 0.2753 (mmt) cc_final: 0.2104 (mpp) REVERT: E 436 MET cc_start: 0.8096 (mpp) cc_final: 0.7859 (mpp) REVERT: F 429 MET cc_start: 0.1898 (mtt) cc_final: 0.1676 (mtm) outliers start: 75 outliers final: 36 residues processed: 190 average time/residue: 0.1772 time to fit residues: 55.0911 Evaluate side-chains 142 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 62 ASP Chi-restraints excluded: chain A residue 126 ASP 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 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 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: 6.9990 chunk 252 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 231 optimal weight: 30.0000 chunk 239 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 299 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 199 optimal weight: 0.0470 overall best weight: 2.8084 ------------------------------------------------------------------------------- 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 B 65 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.123712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.070774 restraints weight = 156296.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.065720 restraints weight = 118602.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.062802 restraints weight = 92693.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.061878 restraints weight = 73235.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.061835 restraints weight = 67142.424| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 27841 Z= 0.210 Angle : 0.785 23.261 38047 Z= 0.395 Chirality : 0.046 0.287 4347 Planarity : 0.005 0.135 4671 Dihedral : 12.520 131.122 4449 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.23 % Favored : 87.50 % Rotamer: Outliers : 3.47 % Allowed : 16.21 % Favored : 80.32 % 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: -3.51 (0.13), residues: 3298 helix: -0.95 (0.15), residues: 1114 sheet: -2.47 (0.24), residues: 377 loop : -3.35 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 560 TYR 0.028 0.002 TYR F 299 PHE 0.018 0.002 PHE B 15 TRP 0.013 0.002 TRP A 598 HIS 0.010 0.002 HIS K 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (27791) covalent geometry : angle 0.74544 / 0.39 (38013) hydrogen bonds : bond 0.06874 / 4.52 ( 1010) hydrogen bonds : angle 6.35060 / 4.36 ( 2757) metal coordination : bond 0.02402 / 1.22 ( 50) metal coordination : angle 8.29583 / 5.83 ( 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 215 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 118 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8115 (t0) REVERT: A 668 MET cc_start: 0.8925 (tmm) cc_final: 0.8342 (ttp) REVERT: A 899 MET cc_start: 0.8361 (mmm) cc_final: 0.7919 (mtp) REVERT: B 62 MET cc_start: 0.8733 (ppp) cc_final: 0.8520 (ppp) REVERT: B 90 MET cc_start: 0.9492 (tmm) cc_final: 0.9172 (tmm) REVERT: K 57 MET cc_start: 0.2375 (mmt) cc_final: 0.1740 (mpp) REVERT: K 62 MET cc_start: 0.1109 (tmm) cc_final: 0.0839 (tmm) REVERT: K 72 MET cc_start: -0.4214 (ttm) cc_final: -0.4461 (ttm) REVERT: E 429 MET cc_start: 0.8100 (mtp) cc_final: 0.7718 (mtp) REVERT: F 293 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5458 (mm) outliers start: 97 outliers final: 60 residues processed: 209 average time/residue: 0.1670 time to fit residues: 57.3365 Evaluate side-chains 168 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 106 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 126 ASP 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 247 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL 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 566 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain 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 166 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 74 ILE 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 E residue 334 ILE Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 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 500 LEU Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 121 optimal weight: 0.0050 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 202 optimal weight: 50.0000 chunk 125 optimal weight: 0.8980 chunk 326 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 291 optimal weight: 20.0000 chunk 172 optimal weight: 0.5980 chunk 177 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 ** 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** F 548 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.123587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.078069 restraints weight = 183879.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070180 restraints weight = 137395.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.069222 restraints weight = 70266.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.068414 restraints weight = 48233.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068760 restraints weight = 47894.450| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 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: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 27841 Z= 0.141 Angle : 0.707 18.318 38047 Z= 0.358 Chirality : 0.043 0.276 4347 Planarity : 0.005 0.055 4671 Dihedral : 12.086 130.454 4447 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.13 % Favored : 91.62 % Rotamer: Outliers : 2.49 % Allowed : 18.07 % Favored : 79.44 % 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: -2.92 (0.14), residues: 3298 helix: -0.37 (0.15), residues: 1126 sheet: -2.22 (0.24), residues: 395 loop : -3.06 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 560 TYR 0.030 0.001 TYR F 299 PHE 0.035 0.002 PHE B 15 TRP 0.014 0.001 TRP A 598 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (27791) covalent geometry : angle 0.68182 / 0.36 (38013) hydrogen bonds : bond 0.06277 / 4.22 ( 1010) hydrogen bonds : angle 5.66468 / 3.93 ( 2757) metal coordination : bond 0.02054 / 1.07 ( 50) metal coordination : angle 6.31973 / 4.31 ( 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 195 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 126 time to evaluate : 1.032 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 110 MET cc_start: 0.8406 (mmm) cc_final: 0.7822 (tpp) REVERT: A 126 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8212 (t0) REVERT: A 454 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8886 (t0) REVERT: A 668 MET cc_start: 0.9017 (tmm) cc_final: 0.8364 (ttp) REVERT: A 899 MET cc_start: 0.8337 (mmm) cc_final: 0.8075 (mmm) REVERT: B 49 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8679 (m-10) REVERT: B 90 MET cc_start: 0.9523 (tmm) cc_final: 0.9236 (tmm) REVERT: D 129 MET cc_start: 0.7752 (mmm) cc_final: 0.7327 (mmm) REVERT: K 57 MET cc_start: 0.2691 (mmt) cc_final: 0.2156 (mpp) REVERT: K 153 MET cc_start: 0.6490 (tpp) cc_final: 0.5625 (tpt) REVERT: E 576 MET cc_start: 0.2364 (mtp) cc_final: 0.1920 (mtm) REVERT: F 293 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6163 (mm) outliers start: 69 outliers final: 32 residues processed: 188 average time/residue: 0.1724 time to fit residues: 53.4606 Evaluate side-chains 143 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 126 ASP 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 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 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 B residue 49 PHE Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 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 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 374 ASP 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 441 CYS Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 532 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 323 optimal weight: 6.9990 chunk 202 optimal weight: 40.0000 chunk 291 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 301 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN A 713 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS ** E 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.123566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081776 restraints weight = 155354.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.073696 restraints weight = 117815.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.072395 restraints weight = 96514.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.072086 restraints weight = 71649.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071337 restraints weight = 60241.619| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 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 = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 27841 Z= 0.249 Angle : 0.743 18.248 38047 Z= 0.372 Chirality : 0.044 0.279 4347 Planarity : 0.005 0.055 4671 Dihedral : 11.990 133.746 4442 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.50 % Favored : 89.23 % Rotamer: Outliers : 3.09 % Allowed : 18.63 % Favored : 78.28 % 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: -2.84 (0.14), residues: 3298 helix: -0.35 (0.15), residues: 1126 sheet: -2.12 (0.25), residues: 369 loop : -2.98 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 579 TYR 0.025 0.002 TYR A 217 PHE 0.038 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 0.00555 / 0.25 (27791) covalent geometry : angle 0.71602 / 0.37 (38013) hydrogen bonds : bond 0.06292 / 4.22 ( 1010) hydrogen bonds : angle 5.84068 / 4.03 ( 2757) metal coordination : bond 0.01632 / 0.83 ( 50) metal coordination : angle 6.67188 / 4.58 ( 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: 86 poor density : 116 time to evaluate : 0.844 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 126 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8297 (t0) REVERT: A 454 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8960 (t0) REVERT: A 668 MET cc_start: 0.9023 (tmm) cc_final: 0.8374 (ttp) REVERT: A 899 MET cc_start: 0.8385 (mmm) cc_final: 0.7732 (ttt) REVERT: B 62 MET cc_start: 0.8649 (ppp) cc_final: 0.8446 (ppp) REVERT: B 90 MET cc_start: 0.9527 (tmm) cc_final: 0.9215 (tmm) REVERT: D 129 MET cc_start: 0.7814 (mmm) cc_final: 0.7481 (mmm) REVERT: K 41 ASP cc_start: 0.5928 (p0) cc_final: 0.5514 (m-30) REVERT: K 57 MET cc_start: 0.2752 (mmt) cc_final: 0.2314 (mpp) REVERT: K 72 MET cc_start: -0.4248 (ttm) cc_final: -0.4470 (ttm) REVERT: E 429 MET cc_start: 0.8517 (mtp) cc_final: 0.7777 (ttt) REVERT: E 516 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6097 (t0) REVERT: F 293 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6502 (mm) outliers start: 86 outliers final: 58 residues processed: 194 average time/residue: 0.1596 time to fit residues: 51.5888 Evaluate side-chains 167 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 105 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 126 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 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 756 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 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 49 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 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 86 ASN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 516 ASN 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 513 SER 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: 0.9990 chunk 174 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 38 optimal weight: 0.0020 overall best weight: 0.8392 ------------------------------------------------------------------------------- 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 ** 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 245 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.123508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.079214 restraints weight = 141459.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072200 restraints weight = 101330.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.070225 restraints weight = 63596.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068776 restraints weight = 41937.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.068704 restraints weight = 39310.880| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27841 Z= 0.129 Angle : 0.661 16.921 38047 Z= 0.333 Chirality : 0.042 0.282 4347 Planarity : 0.004 0.056 4671 Dihedral : 11.844 132.154 4442 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.13 % Favored : 91.65 % Rotamer: Outliers : 2.81 % Allowed : 19.47 % 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: -2.50 (0.14), residues: 3298 helix: -0.03 (0.16), residues: 1119 sheet: -1.91 (0.26), residues: 373 loop : -2.80 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 560 TYR 0.020 0.001 TYR F 299 PHE 0.032 0.001 PHE B 15 TRP 0.014 0.001 TRP A 598 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (27791) covalent geometry : angle 0.63800 / 0.33 (38013) hydrogen bonds : bond 0.06039 / 4.10 ( 1010) hydrogen bonds : angle 5.40517 / 3.75 ( 2757) metal coordination : bond 0.01709 / 0.92 ( 50) metal coordination : angle 5.75343 / 3.90 ( 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: 78 poor density : 122 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8378 (mmm) cc_final: 0.7484 (tpp) REVERT: A 454 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8813 (t0) REVERT: A 668 MET cc_start: 0.8981 (tmm) cc_final: 0.8344 (ttp) REVERT: B 62 MET cc_start: 0.8463 (ppp) cc_final: 0.8231 (ppp) REVERT: B 90 MET cc_start: 0.9473 (tmm) cc_final: 0.9237 (tmm) REVERT: B 94 MET cc_start: 0.8709 (ppp) cc_final: 0.8471 (ppp) REVERT: D 129 MET cc_start: 0.7593 (mmm) cc_final: 0.7190 (mmm) REVERT: K 57 MET cc_start: 0.2676 (mmt) cc_final: 0.2162 (mpp) REVERT: K 241 MET cc_start: -0.1584 (mtm) cc_final: -0.1895 (mpp) REVERT: E 516 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.6914 (t0) REVERT: F 293 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6243 (mm) outliers start: 78 outliers final: 51 residues processed: 196 average time/residue: 0.1771 time to fit residues: 58.7427 Evaluate side-chains 164 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 110 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL 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 786 LEU 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 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 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 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 255 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 516 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 182 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 331 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 324 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** 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 713 ASN A 928 HIS ** C 19 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 11 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.122607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.078495 restraints weight = 170693.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.070859 restraints weight = 129226.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.069964 restraints weight = 100786.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.069479 restraints weight = 70379.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.068627 restraints weight = 74151.752| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 27841 Z= 0.344 Angle : 0.804 18.499 38047 Z= 0.404 Chirality : 0.046 0.285 4347 Planarity : 0.005 0.055 4671 Dihedral : 11.881 135.529 4442 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.90 % Favored : 88.86 % Rotamer: Outliers : 3.16 % Allowed : 19.68 % Favored : 77.16 % 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: -2.75 (0.14), residues: 3298 helix: -0.36 (0.15), residues: 1127 sheet: -2.07 (0.26), residues: 372 loop : -2.87 (0.13), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 57 TYR 0.032 0.002 TYR A 217 PHE 0.029 0.002 PHE B 15 TRP 0.010 0.002 TRP A 598 HIS 0.009 0.002 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.34 (27791) covalent geometry : angle 0.77807 / 0.40 (38013) hydrogen bonds : bond 0.06428 / 4.31 ( 1010) hydrogen bonds : angle 5.86668 / 4.05 ( 2757) metal coordination : bond 0.01630 / 0.86 ( 50) metal coordination : angle 6.82186 / 4.72 ( 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 202 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 114 time to evaluate : 1.084 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: 0.8081 (mmm) cc_final: 0.7355 (tpp) REVERT: A 163 TYR cc_start: 0.9255 (OUTLIER) cc_final: 0.8678 (p90) REVERT: A 668 MET cc_start: 0.8921 (tmm) cc_final: 0.8291 (ttp) REVERT: B 90 MET cc_start: 0.9451 (tmm) cc_final: 0.9162 (tmm) REVERT: D 129 MET cc_start: 0.7733 (mmm) cc_final: 0.7526 (mmm) REVERT: K 57 MET cc_start: 0.2775 (mmt) cc_final: 0.2330 (mpp) REVERT: E 414 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8515 (tmtt) REVERT: E 429 MET cc_start: 0.8470 (mtp) cc_final: 0.7931 (mtp) REVERT: E 516 ASN cc_start: 0.6840 (OUTLIER) cc_final: 0.6137 (t0) REVERT: F 293 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6372 (mm) outliers start: 88 outliers final: 62 residues processed: 196 average time/residue: 0.1716 time to fit residues: 55.8599 Evaluate side-chains 170 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 105 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 163 TYR 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 261 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 23 GLU 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 D residue 78 ASP Chi-restraints excluded: chain D residue 106 ILE 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 7 LEU 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 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 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 477 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain F residue 2 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 14 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 326 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 chunk 249 optimal weight: 0.0980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN ** A 295 HIS ** 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 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.124559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.074997 restraints weight = 161448.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.068506 restraints weight = 127526.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.065830 restraints weight = 99689.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065458 restraints weight = 72987.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.063644 restraints weight = 65766.060| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27841 Z= 0.176 Angle : 0.709 18.048 38047 Z= 0.355 Chirality : 0.043 0.334 4347 Planarity : 0.004 0.055 4671 Dihedral : 11.798 134.020 4442 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.07 % Favored : 90.71 % Rotamer: Outliers : 2.70 % Allowed : 20.07 % Favored : 77.23 % 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: -2.55 (0.14), residues: 3298 helix: -0.14 (0.15), residues: 1124 sheet: -1.98 (0.26), residues: 377 loop : -2.77 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 75 TYR 0.019 0.001 TYR E 253 PHE 0.027 0.002 PHE B 15 TRP 0.012 0.001 TRP A 598 HIS 0.008 0.001 HIS K 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (27791) covalent geometry : angle 0.68365 / 0.35 (38013) hydrogen bonds : bond 0.06153 / 4.18 ( 1010) hydrogen bonds : angle 5.54643 / 3.84 ( 2757) metal coordination : bond 0.01655 / 0.87 ( 50) metal coordination : angle 6.32301 / 4.36 ( 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 189 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 114 time to evaluate : 1.029 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 668 MET cc_start: 0.9074 (tmm) cc_final: 0.8326 (ttp) REVERT: B 90 MET cc_start: 0.9526 (tmm) cc_final: 0.9238 (tmm) REVERT: D 129 MET cc_start: 0.7876 (mmm) cc_final: 0.7449 (mmm) REVERT: K 57 MET cc_start: 0.2540 (mmt) cc_final: 0.2152 (mpp) REVERT: K 72 MET cc_start: -0.3082 (ttm) cc_final: -0.3669 (ttt) REVERT: K 241 MET cc_start: -0.0824 (mtm) cc_final: -0.1079 (mpp) REVERT: E 516 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7187 (t0) REVERT: F 11 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: F 293 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5906 (mm) outliers start: 75 outliers final: 61 residues processed: 185 average time/residue: 0.1684 time to fit residues: 52.3894 Evaluate side-chains 170 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 106 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 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 786 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain 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 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 K residue 7 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 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 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 387 VAL Chi-restraints excluded: chain E residue 477 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 56 optimal weight: 5.9990 chunk 303 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 179 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 297 optimal weight: 6.9990 chunk 208 optimal weight: 0.0040 chunk 241 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** 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 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.125536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.088417 restraints weight = 158045.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.082054 restraints weight = 112944.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081169 restraints weight = 81069.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.081011 restraints weight = 57899.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080700 restraints weight = 51240.285| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27841 Z= 0.132 Angle : 0.672 15.395 38047 Z= 0.335 Chirality : 0.042 0.281 4347 Planarity : 0.004 0.056 4671 Dihedral : 11.636 133.134 4442 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.68 % Favored : 91.11 % Rotamer: Outliers : 2.21 % Allowed : 20.53 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.19 % Twisted Proline : 0.71 % 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: -2.35 (0.14), residues: 3298 helix: 0.02 (0.15), residues: 1132 sheet: -1.80 (0.25), residues: 395 loop : -2.68 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 75 TYR 0.015 0.001 TYR F 299 PHE 0.025 0.001 PHE B 15 TRP 0.027 0.001 TRP K 186 HIS 0.011 0.001 HIS K 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (27791) covalent geometry : angle 0.64593 / 0.33 (38013) hydrogen bonds : bond 0.06013 / 4.12 ( 1010) hydrogen bonds : angle 5.28031 / 3.67 ( 2757) metal coordination : bond 0.01779 / 1.04 ( 50) metal coordination : angle 6.24885 / 4.22 ( 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 172 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 111 time to evaluate : 1.058 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: 0.8287 (mmm) cc_final: 0.7144 (tpp) REVERT: A 668 MET cc_start: 0.9061 (tmm) cc_final: 0.8352 (ttp) REVERT: B 90 MET cc_start: 0.9460 (tmm) cc_final: 0.9238 (tmm) REVERT: K 57 MET cc_start: 0.2831 (mmt) cc_final: 0.2455 (mpp) REVERT: K 241 MET cc_start: -0.1918 (mtm) cc_final: -0.2442 (mpp) REVERT: E 233 MET cc_start: 0.8286 (ppp) cc_final: 0.7887 (ppp) REVERT: E 516 ASN cc_start: 0.6156 (OUTLIER) cc_final: 0.5500 (t0) REVERT: E 534 ASP cc_start: 0.6576 (m-30) cc_final: 0.6310 (t0) REVERT: F 11 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8178 (mp10) outliers start: 61 outliers final: 52 residues processed: 169 average time/residue: 0.1715 time to fit residues: 48.3910 Evaluate side-chains 161 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 107 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 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 B residue 83 VAL 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 182 TRP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 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 253 LEU 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 477 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 306 optimal weight: 8.9990 chunk 164 optimal weight: 40.0000 chunk 85 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 117 optimal weight: 0.0060 chunk 119 optimal weight: 7.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** 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 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.122899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.070267 restraints weight = 156833.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.068063 restraints weight = 91453.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064273 restraints weight = 67249.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.064155 restraints weight = 56544.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.063481 restraints weight = 50690.461| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27841 Z= 0.153 Angle : 0.675 14.757 38047 Z= 0.335 Chirality : 0.042 0.280 4347 Planarity : 0.004 0.057 4671 Dihedral : 11.560 133.832 4442 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.50 % Favored : 91.29 % Rotamer: Outliers : 2.25 % Allowed : 20.39 % Favored : 77.37 % 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: -2.30 (0.14), residues: 3298 helix: 0.04 (0.15), residues: 1132 sheet: -1.81 (0.25), residues: 402 loop : -2.62 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 75 TYR 0.017 0.001 TYR A 217 PHE 0.024 0.001 PHE B 15 TRP 0.025 0.001 TRP K 186 HIS 0.006 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (27791) covalent geometry : angle 0.65020 / 0.33 (38013) hydrogen bonds : bond 0.05928 / 4.05 ( 1010) hydrogen bonds : angle 5.26196 / 3.66 ( 2757) metal coordination : bond 0.01632 / 0.94 ( 50) metal coordination : angle 6.10430 / 4.08 ( 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 170 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 108 time to evaluate : 1.003 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: 0.8631 (mmm) cc_final: 0.7691 (tpp) REVERT: A 668 MET cc_start: 0.9070 (tmm) cc_final: 0.8347 (ttp) REVERT: B 90 MET cc_start: 0.9463 (tmm) cc_final: 0.9242 (tmm) REVERT: K 57 MET cc_start: 0.2554 (mmt) cc_final: 0.2183 (mpp) REVERT: K 241 MET cc_start: -0.1140 (mtm) cc_final: -0.1557 (mpp) REVERT: E 516 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7478 (t0) REVERT: F 11 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8223 (mp10) outliers start: 62 outliers final: 57 residues processed: 167 average time/residue: 0.1634 time to fit residues: 45.7876 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 : 0.909 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR 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 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 97 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 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 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 477 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 592 ILE Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 441 CYS Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 590 LEU 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: 20.0000 chunk 229 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 306 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 291 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** 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 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.123254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081827 restraints weight = 159024.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.074626 restraints weight = 117567.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.073060 restraints weight = 100062.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.072914 restraints weight = 77309.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072631 restraints weight = 66041.808| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 27841 Z= 0.274 Angle : 0.764 15.686 38047 Z= 0.379 Chirality : 0.045 0.283 4347 Planarity : 0.005 0.056 4671 Dihedral : 11.609 135.247 4442 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.08 % Favored : 89.68 % Rotamer: Outliers : 2.56 % Allowed : 20.28 % Favored : 77.16 % 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: -2.45 (0.14), residues: 3298 helix: -0.18 (0.15), residues: 1131 sheet: -1.84 (0.26), residues: 362 loop : -2.65 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 75 TYR 0.027 0.002 TYR A 217 PHE 0.024 0.002 PHE B 15 TRP 0.028 0.002 TRP K 186 HIS 0.009 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (27791) covalent geometry : angle 0.73864 / 0.38 (38013) hydrogen bonds : bond 0.06152 / 4.17 ( 1010) hydrogen bonds : angle 5.54839 / 3.84 ( 2757) metal coordination : bond 0.01587 / 0.89 ( 50) metal coordination : angle 6.56235 / 4.41 ( 34) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9805.90 seconds wall clock time: 168 minutes 10.50 seconds (10090.50 seconds total)