Starting phenix.real_space_refine on Sun Feb 18 07:53:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxn_30493/02_2024/7cxn_30493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxn_30493/02_2024/7cxn_30493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxn_30493/02_2024/7cxn_30493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxn_30493/02_2024/7cxn_30493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxn_30493/02_2024/7cxn_30493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxn_30493/02_2024/7cxn_30493.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 57 5.49 5 S 149 5.16 5 C 13292 2.51 5 N 3614 2.21 5 O 4175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 540": "OE1" <-> "OE2" Residue "E GLU 551": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21295 Number of models: 1 Model: "" Number of chains: 12 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 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, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "L" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 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: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 59.044 66.687 125.669 1.00120.79 S ATOM 2487 SG CYS A 306 58.337 66.866 129.473 1.00109.02 S ATOM 2519 SG CYS A 310 61.753 65.606 128.086 1.00106.10 S ATOM 3927 SG CYS A 487 48.124 78.989 112.682 1.00132.82 S ATOM 5180 SG CYS A 645 47.855 80.227 116.275 1.00129.11 S ATOM 5186 SG CYS A 646 48.897 76.635 115.582 1.00129.46 S ATOM 12066 SG CYS F 5 38.526 77.166 65.507 1.00197.03 S ATOM 12087 SG CYS F 8 39.371 79.862 62.949 1.00196.81 S ATOM 12225 SG CYS F 26 36.565 80.652 64.966 1.00207.13 S ATOM 12246 SG CYS F 29 35.663 78.053 63.206 1.00212.00 S ATOM 12411 SG CYS F 50 23.804 84.901 87.278 1.00252.93 S ATOM 12441 SG CYS F 55 20.831 82.494 87.526 1.00257.68 S ATOM 12574 SG CYS F 72 20.226 85.818 86.079 1.00263.37 S ATOM 12148 SG CYS F 16 31.023 72.587 73.118 1.00204.79 S ATOM 12163 SG CYS F 19 32.116 69.541 71.286 1.00214.40 S ATOM 16696 SG CYS E 5 77.272 115.943 58.881 1.00140.71 S ATOM 16717 SG CYS E 8 79.506 119.058 58.914 1.00146.09 S ATOM 16855 SG CYS E 26 75.589 119.357 59.219 1.00149.43 S ATOM 16876 SG CYS E 29 76.948 118.751 56.213 1.00156.27 S ATOM 17041 SG CYS E 50 49.379 115.931 58.356 1.00185.29 S ATOM 17071 SG CYS E 55 49.243 116.075 54.577 1.00193.67 S ATOM 17204 SG CYS E 72 48.122 119.109 56.517 1.00184.60 S ATOM 16778 SG CYS E 16 68.067 112.253 51.573 1.00144.79 S ATOM 16793 SG CYS E 19 70.696 110.872 49.344 1.00147.10 S Time building chain proxies: 10.69, per 1000 atoms: 0.50 Number of scatterers: 21295 At special positions: 0 Unit cell: (139.4, 159.9, 187.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 149 16.00 P 57 15.00 O 4175 8.00 N 3614 7.00 C 13292 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 - 3.50 Amino acid : False - 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: 9.89 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " Number of angles added : 28 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 22 sheets defined 42.8% alpha, 12.5% beta 20 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 8.00 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.755A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (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 77 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.515A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.505A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.600A pdb=" N ASN A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.551A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.523A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.768A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.334A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.511A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.722A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 4.280A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.199A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.185A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.715A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 468 through 479 removed outlier: 4.415A 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 519 removed outlier: 4.163A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.577A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.536A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.836A pdb=" N PHE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 791 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.562A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 854 removed outlier: 3.502A pdb=" N LEU A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 854' Processing helix chain 'A' and resid 855 through 866 removed outlier: 4.102A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 875 through 903 removed outlier: 3.616A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.388A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 31 through 43 removed outlier: 4.631A pdb=" N SER B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 54 through 96 removed outlier: 3.658A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.670A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.951A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 45 through 62 removed outlier: 3.948A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.604A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.573A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 42 through 80 removed outlier: 4.766A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 6.017A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.557A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.708A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.912A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 275 removed outlier: 4.250A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 4.363A pdb=" N HIS F 290 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 4.948A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 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 446 through 451 removed outlier: 3.747A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 495 through 500 removed outlier: 4.821A pdb=" N GLU F 498 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.526A pdb=" N ALA F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 567 removed outlier: 3.626A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 584 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.934A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.526A pdb=" N PHE E 262 " --> pdb=" O SER E 259 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER E 264 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 286 through 299 removed outlier: 4.081A pdb=" N HIS E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.765A pdb=" N TYR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 375 through 379 Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 431 Processing helix chain 'E' and resid 445 through 454 Processing helix chain 'E' and resid 489 through 501 removed outlier: 3.682A pdb=" N ILE E 493 " --> pdb=" O ASN E 489 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 501 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 525 Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 580 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.963A pdb=" N PHE A 45 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 37 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 47 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 35 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 49 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG A 33 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR A 51 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 31 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS A 53 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 12.460A pdb=" N LYS A 50 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N ARG A 74 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN A 52 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 72 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS A 54 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE A 70 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 66 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.706A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.648A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.502A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.689A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP D 143 " --> pdb=" O THR D 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 152 through 156 removed outlier: 6.994A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 209 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY F 184 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU F 197 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE F 182 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 277 through 278 removed outlier: 6.665A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 470 through 472 removed outlier: 5.953A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 470 through 472 removed outlier: 8.360A pdb=" N ASP F 542 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE F 572 " --> pdb=" O ASP F 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.602A pdb=" N THR E 12 " --> pdb=" O GLY E 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'E' and resid 163 through 167 removed outlier: 7.118A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP E 223 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 201 through 202 Processing sheet with id=AC3, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.579A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 399 " --> pdb=" O PHE E 373 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS E 358 " --> pdb=" O TYR E 306 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 470 through 471 removed outlier: 6.601A pdb=" N CYS E 471 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 544 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE E 575 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE E 546 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 789 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 7.81 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6508 1.33 - 1.46: 5384 1.46 - 1.58: 9653 1.58 - 1.71: 111 1.71 - 1.83: 210 Bond restraints: 21866 Sorted by residual: bond pdb=" CA LEU A 302 " pdb=" CB LEU A 302 " ideal model delta sigma weight residual 1.531 1.361 0.170 1.57e-02 4.06e+03 1.17e+02 bond pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta sigma weight residual 1.526 1.414 0.113 1.28e-02 6.10e+03 7.75e+01 bond pdb=" CA TRP A 509 " pdb=" C TRP A 509 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.34e-02 5.57e+03 2.73e+01 bond pdb=" N GLY A 510 " pdb=" CA GLY A 510 " ideal model delta sigma weight residual 1.447 1.508 -0.061 1.19e-02 7.06e+03 2.60e+01 bond pdb=" CA LYS A 718 " pdb=" C LYS A 718 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.17e+01 ... (remaining 21861 not shown) Histogram of bond angle deviations from ideal: 89.97 - 99.03: 14 99.03 - 108.09: 1507 108.09 - 117.16: 14583 117.16 - 126.22: 13468 126.22 - 135.28: 408 Bond angle restraints: 29980 Sorted by residual: angle pdb=" N ILE E 333 " pdb=" CA ILE E 333 " pdb=" C ILE E 333 " ideal model delta sigma weight residual 111.81 125.42 -13.61 8.60e-01 1.35e+00 2.51e+02 angle pdb=" N ASP A 303 " pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta sigma weight residual 108.96 128.27 -19.31 1.23e+00 6.61e-01 2.46e+02 angle pdb=" N PHE A 275 " pdb=" CA PHE A 275 " pdb=" C PHE A 275 " ideal model delta sigma weight residual 111.54 129.11 -17.57 1.36e+00 5.41e-01 1.67e+02 angle pdb=" N VAL F 348 " pdb=" CA VAL F 348 " pdb=" C VAL F 348 " ideal model delta sigma weight residual 111.58 124.09 -12.51 1.06e+00 8.90e-01 1.39e+02 angle pdb=" N GLN D 157 " pdb=" CA GLN D 157 " pdb=" CB GLN D 157 " ideal model delta sigma weight residual 110.90 95.33 15.57 1.33e+00 5.65e-01 1.37e+02 ... (remaining 29975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 12585 27.42 - 54.84: 486 54.84 - 82.26: 107 82.26 - 109.68: 5 109.68 - 137.10: 1 Dihedral angle restraints: 13184 sinusoidal: 5598 harmonic: 7586 Sorted by residual: dihedral pdb=" C ASP E 344 " pdb=" N ASP E 344 " pdb=" CA ASP E 344 " pdb=" CB ASP E 344 " ideal model delta harmonic sigma weight residual -122.60 -144.90 22.30 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" N ASP E 344 " pdb=" C ASP E 344 " pdb=" CA ASP E 344 " pdb=" CB ASP E 344 " ideal model delta harmonic sigma weight residual 122.80 143.05 -20.25 0 2.50e+00 1.60e-01 6.56e+01 dihedral pdb=" N ASP A 303 " pdb=" C ASP A 303 " pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta harmonic sigma weight residual 122.80 141.10 -18.30 0 2.50e+00 1.60e-01 5.36e+01 ... (remaining 13181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 3416 0.201 - 0.403: 36 0.403 - 0.604: 8 0.604 - 0.805: 3 0.805 - 1.006: 2 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CA ASP E 344 " pdb=" N ASP E 344 " pdb=" C ASP E 344 " pdb=" CB ASP E 344 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.53e+01 chirality pdb=" CA LEU A 302 " pdb=" N LEU A 302 " pdb=" C LEU A 302 " pdb=" CB LEU A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CA ASP A 303 " pdb=" N ASP A 303 " pdb=" C ASP A 303 " pdb=" CB ASP A 303 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.80 2.00e-01 2.50e+01 1.58e+01 ... (remaining 3462 not shown) Planarity restraints: 3626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO B 183 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 173 " 0.038 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO F 174 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 132 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 133 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 ... (remaining 3623 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 247 2.42 - 3.04: 15799 3.04 - 3.66: 34744 3.66 - 4.28: 49695 4.28 - 4.90: 75997 Nonbonded interactions: 176482 Sorted by model distance: nonbonded pdb=" CD ARG F 332 " pdb=" O LYS F 347 " model vdw 1.804 3.440 nonbonded pdb=" ND2 ASN F 124 " pdb=" O TYR F 421 " model vdw 1.977 2.520 nonbonded pdb=" OG1 THR E 153 " pdb=" OG SER E 166 " model vdw 2.044 2.440 nonbonded pdb=" O ASP A 846 " pdb=" OG1 THR A 850 " model vdw 2.049 2.440 nonbonded pdb=" O ASP E 260 " pdb=" OG SER E 263 " model vdw 2.087 2.440 ... (remaining 176477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 596 or resid 701 through 703)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 596 or resid 1000 through 1002)) } 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=1.00 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.240 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 68.910 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 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 : 0.007 0.170 21866 Z= 0.487 Angle : 1.126 24.482 29980 Z= 0.693 Chirality : 0.067 1.006 3465 Planarity : 0.005 0.107 3626 Dihedral : 15.247 137.102 8290 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.90 % Favored : 86.71 % Rotamer: Outliers : 0.23 % Allowed : 7.44 % Favored : 92.33 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.13), residues: 2551 helix: -2.69 (0.12), residues: 954 sheet: -2.17 (0.29), residues: 244 loop : -3.60 (0.13), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 182 HIS 0.008 0.001 HIS A 75 PHE 0.016 0.002 PHE A 753 TYR 0.022 0.002 TYR A 689 ARG 0.005 0.000 ARG F 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 2.668 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 242 MET cc_start: 0.9297 (mtt) cc_final: 0.8990 (mtm) REVERT: A 615 MET cc_start: 0.8571 (ptm) cc_final: 0.8248 (ppp) REVERT: A 633 MET cc_start: 0.8974 (tmm) cc_final: 0.8577 (tmm) REVERT: A 668 MET cc_start: 0.9522 (tmm) cc_final: 0.8839 (tmm) REVERT: A 902 MET cc_start: 0.8799 (ttt) cc_final: 0.8586 (ttt) REVERT: B 67 MET cc_start: 0.9415 (ttm) cc_final: 0.9066 (tmm) REVERT: B 142 CYS cc_start: 0.8457 (p) cc_final: 0.8114 (p) REVERT: D 55 MET cc_start: 0.9438 (tmm) cc_final: 0.9034 (tmm) REVERT: D 65 GLN cc_start: 0.9487 (pt0) cc_final: 0.8933 (pp30) REVERT: D 67 MET cc_start: 0.9162 (mtm) cc_final: 0.8812 (mtm) REVERT: D 88 GLN cc_start: 0.9412 (mt0) cc_final: 0.9085 (mp10) REVERT: D 94 MET cc_start: 0.8918 (mtp) cc_final: 0.8577 (ttm) REVERT: D 158 GLN cc_start: 0.8919 (tt0) cc_final: 0.8634 (tm-30) REVERT: F 68 MET cc_start: 0.8931 (pmm) cc_final: 0.8608 (pmm) REVERT: F 378 MET cc_start: 0.8763 (tpp) cc_final: 0.8120 (tpp) REVERT: F 455 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7580 (pp) REVERT: E 363 LEU cc_start: 0.9574 (mt) cc_final: 0.9240 (mt) REVERT: E 561 PHE cc_start: 0.9382 (t80) cc_final: 0.9152 (t80) outliers start: 5 outliers final: 2 residues processed: 179 average time/residue: 0.3964 time to fit residues: 104.4076 Evaluate side-chains 118 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 3.9990 chunk 194 optimal weight: 0.2980 chunk 108 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN D 100 ASN D 108 ASN D 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN F 281 GLN ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS E 518 GLN E 519 ASN E 531 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21866 Z= 0.179 Angle : 0.685 13.573 29980 Z= 0.361 Chirality : 0.042 0.232 3465 Planarity : 0.005 0.064 3626 Dihedral : 13.168 132.369 3684 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.74 % Favored : 91.02 % Rotamer: Outliers : 1.50 % Allowed : 12.35 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.15), residues: 2551 helix: -0.61 (0.16), residues: 966 sheet: -1.77 (0.28), residues: 280 loop : -2.80 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 182 HIS 0.015 0.001 HIS A 75 PHE 0.024 0.001 PHE B 15 TYR 0.016 0.001 TYR E 582 ARG 0.005 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 2.523 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 633 MET cc_start: 0.8825 (tmm) cc_final: 0.8533 (tmm) REVERT: A 668 MET cc_start: 0.9489 (tmm) cc_final: 0.8825 (tmm) REVERT: B 49 PHE cc_start: 0.9390 (t80) cc_final: 0.9116 (m-80) REVERT: B 62 MET cc_start: 0.9304 (ppp) cc_final: 0.9013 (ppp) REVERT: B 67 MET cc_start: 0.9412 (ttm) cc_final: 0.9055 (tmm) REVERT: B 142 CYS cc_start: 0.8577 (p) cc_final: 0.8011 (p) REVERT: D 48 GLU cc_start: 0.9129 (pt0) cc_final: 0.8529 (tm-30) REVERT: D 55 MET cc_start: 0.9531 (tmm) cc_final: 0.9193 (tmm) REVERT: D 65 GLN cc_start: 0.9368 (pt0) cc_final: 0.8913 (pp30) REVERT: D 67 MET cc_start: 0.9031 (mtm) cc_final: 0.8795 (mtm) REVERT: D 88 GLN cc_start: 0.9270 (mt0) cc_final: 0.8986 (mp10) REVERT: F 68 MET cc_start: 0.8943 (pmm) cc_final: 0.8612 (pmm) REVERT: F 304 ILE cc_start: 0.9087 (mt) cc_final: 0.8819 (mm) REVERT: F 378 MET cc_start: 0.8842 (tpp) cc_final: 0.8201 (tpp) REVERT: E 295 LEU cc_start: 0.9788 (tp) cc_final: 0.9533 (pp) REVERT: E 363 LEU cc_start: 0.9552 (mt) cc_final: 0.9164 (mt) REVERT: E 436 MET cc_start: 0.7659 (ptp) cc_final: 0.7255 (ptp) REVERT: E 561 PHE cc_start: 0.9324 (t80) cc_final: 0.9121 (t80) outliers start: 33 outliers final: 10 residues processed: 172 average time/residue: 0.3350 time to fit residues: 90.4217 Evaluate side-chains 127 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 79 optimal weight: 0.1980 chunk 187 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21866 Z= 0.264 Angle : 0.661 13.466 29980 Z= 0.347 Chirality : 0.041 0.216 3465 Planarity : 0.004 0.058 3626 Dihedral : 12.920 136.503 3683 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.86 % Favored : 88.98 % Rotamer: Outliers : 2.09 % Allowed : 15.21 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.16), residues: 2551 helix: 0.01 (0.17), residues: 953 sheet: -1.66 (0.28), residues: 284 loop : -2.51 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 916 HIS 0.013 0.001 HIS A 75 PHE 0.021 0.001 PHE B 15 TYR 0.017 0.001 TYR A 237 ARG 0.006 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 2.329 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 377 ASP cc_start: 0.8703 (t0) cc_final: 0.8466 (t0) REVERT: A 633 MET cc_start: 0.8988 (tmm) cc_final: 0.8737 (tmm) REVERT: A 668 MET cc_start: 0.9484 (tmm) cc_final: 0.8803 (tmm) REVERT: A 902 MET cc_start: 0.8707 (ttt) cc_final: 0.8298 (tmm) REVERT: A 924 MET cc_start: 0.9563 (mmm) cc_final: 0.9195 (mmm) REVERT: D 48 GLU cc_start: 0.9120 (pt0) cc_final: 0.8553 (tm-30) REVERT: D 55 MET cc_start: 0.9542 (tmm) cc_final: 0.9172 (tmm) REVERT: D 65 GLN cc_start: 0.9432 (pt0) cc_final: 0.8956 (pp30) REVERT: D 67 MET cc_start: 0.9032 (mtm) cc_final: 0.8764 (mtm) REVERT: D 70 MET cc_start: 0.9422 (tpp) cc_final: 0.8981 (tmm) REVERT: D 88 GLN cc_start: 0.9298 (mt0) cc_final: 0.9058 (mp10) REVERT: D 90 MET cc_start: 0.9460 (ttp) cc_final: 0.9058 (tmm) REVERT: D 94 MET cc_start: 0.8852 (mtm) cc_final: 0.7610 (mtp) REVERT: D 174 MET cc_start: 0.8756 (pmm) cc_final: 0.8553 (pmm) REVERT: F 68 MET cc_start: 0.8823 (pmm) cc_final: 0.8494 (pmm) REVERT: F 304 ILE cc_start: 0.9175 (mt) cc_final: 0.8939 (mm) REVERT: F 378 MET cc_start: 0.8859 (tpp) cc_final: 0.8118 (tpp) REVERT: F 576 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6346 (tmm) REVERT: E 363 LEU cc_start: 0.9605 (mt) cc_final: 0.9190 (mt) REVERT: E 561 PHE cc_start: 0.9356 (t80) cc_final: 0.9145 (t80) outliers start: 46 outliers final: 24 residues processed: 164 average time/residue: 0.3345 time to fit residues: 86.1497 Evaluate side-chains 136 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 0.0570 chunk 175 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 234 optimal weight: 0.0060 chunk 248 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 557 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21866 Z= 0.159 Angle : 0.610 13.556 29980 Z= 0.318 Chirality : 0.040 0.208 3465 Planarity : 0.004 0.054 3626 Dihedral : 12.772 132.380 3683 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.88 % Favored : 91.96 % Rotamer: Outliers : 1.63 % Allowed : 16.11 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2551 helix: 0.43 (0.17), residues: 955 sheet: -1.11 (0.29), residues: 291 loop : -2.19 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 916 HIS 0.009 0.001 HIS A 75 PHE 0.018 0.001 PHE B 15 TYR 0.011 0.001 TYR A 237 ARG 0.010 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 2.530 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 370 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8787 (pt0) REVERT: A 377 ASP cc_start: 0.8603 (t0) cc_final: 0.8347 (t0) REVERT: A 633 MET cc_start: 0.8865 (tmm) cc_final: 0.8591 (tmm) REVERT: A 668 MET cc_start: 0.9459 (tmm) cc_final: 0.9086 (tmm) REVERT: A 902 MET cc_start: 0.8682 (ttt) cc_final: 0.8331 (tmm) REVERT: A 924 MET cc_start: 0.9499 (mmm) cc_final: 0.9065 (mmm) REVERT: B 49 PHE cc_start: 0.9319 (t80) cc_final: 0.9074 (m-80) REVERT: B 62 MET cc_start: 0.9304 (ppp) cc_final: 0.9075 (ppp) REVERT: B 82 LYS cc_start: 0.9048 (ptpp) cc_final: 0.8822 (ptpp) REVERT: D 48 GLU cc_start: 0.9136 (pt0) cc_final: 0.8513 (tm-30) REVERT: D 55 MET cc_start: 0.9528 (tmm) cc_final: 0.9153 (tmm) REVERT: D 65 GLN cc_start: 0.9407 (pt0) cc_final: 0.8969 (pp30) REVERT: D 67 MET cc_start: 0.9006 (mtm) cc_final: 0.8760 (mtm) REVERT: D 70 MET cc_start: 0.9406 (tpp) cc_final: 0.8951 (tmm) REVERT: D 90 MET cc_start: 0.9381 (ttp) cc_final: 0.8971 (tmm) REVERT: D 94 MET cc_start: 0.8811 (mtm) cc_final: 0.7338 (mtp) REVERT: F 68 MET cc_start: 0.8812 (pmm) cc_final: 0.8541 (pmm) REVERT: F 295 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9538 (mt) REVERT: F 304 ILE cc_start: 0.9156 (mt) cc_final: 0.8956 (mm) REVERT: F 378 MET cc_start: 0.8865 (tpp) cc_final: 0.8134 (tpp) REVERT: F 576 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.6146 (tmm) REVERT: E 295 LEU cc_start: 0.9808 (tp) cc_final: 0.9497 (pp) REVERT: E 363 LEU cc_start: 0.9581 (mt) cc_final: 0.9175 (mt) REVERT: E 436 MET cc_start: 0.7767 (ptp) cc_final: 0.7393 (ptm) REVERT: E 585 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8500 (pp) outliers start: 36 outliers final: 14 residues processed: 171 average time/residue: 0.3496 time to fit residues: 93.2374 Evaluate side-chains 137 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 585 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 102 optimal weight: 0.1980 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21866 Z= 0.259 Angle : 0.640 13.473 29980 Z= 0.333 Chirality : 0.040 0.200 3465 Planarity : 0.004 0.057 3626 Dihedral : 12.688 134.921 3681 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.96 % Favored : 89.93 % Rotamer: Outliers : 2.41 % Allowed : 17.11 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2551 helix: 0.48 (0.17), residues: 957 sheet: -1.18 (0.29), residues: 289 loop : -2.15 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 182 HIS 0.011 0.001 HIS A 75 PHE 0.024 0.001 PHE B 147 TYR 0.017 0.001 TYR A 237 ARG 0.007 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 124 time to evaluate : 2.276 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 633 MET cc_start: 0.8964 (tmm) cc_final: 0.8603 (tmm) REVERT: A 668 MET cc_start: 0.9471 (tmm) cc_final: 0.9039 (tmm) REVERT: A 902 MET cc_start: 0.8709 (ttt) cc_final: 0.8165 (tmm) REVERT: B 49 PHE cc_start: 0.9319 (t80) cc_final: 0.9051 (m-80) REVERT: B 67 MET cc_start: 0.9003 (ppp) cc_final: 0.8799 (tmm) REVERT: B 82 LYS cc_start: 0.9095 (ptpp) cc_final: 0.8885 (pttm) REVERT: B 142 CYS cc_start: 0.8626 (p) cc_final: 0.8231 (p) REVERT: D 48 GLU cc_start: 0.9129 (pt0) cc_final: 0.8509 (tm-30) REVERT: D 55 MET cc_start: 0.9538 (tmm) cc_final: 0.9146 (tmm) REVERT: D 65 GLN cc_start: 0.9411 (pt0) cc_final: 0.9092 (pp30) REVERT: D 67 MET cc_start: 0.9055 (mtm) cc_final: 0.8715 (mtm) REVERT: D 70 MET cc_start: 0.9417 (tpp) cc_final: 0.8990 (tmm) REVERT: D 90 MET cc_start: 0.9447 (ttp) cc_final: 0.9060 (tmm) REVERT: D 94 MET cc_start: 0.8864 (mtm) cc_final: 0.7683 (mtp) REVERT: F 68 MET cc_start: 0.8814 (pmm) cc_final: 0.8520 (pmm) REVERT: F 295 LEU cc_start: 0.9814 (OUTLIER) cc_final: 0.9560 (mt) REVERT: F 378 MET cc_start: 0.8886 (tpp) cc_final: 0.8153 (tpp) REVERT: F 474 MET cc_start: 0.7638 (mmt) cc_final: 0.7281 (mmp) REVERT: F 576 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6163 (tmm) REVERT: E 363 LEU cc_start: 0.9611 (mt) cc_final: 0.9189 (mt) REVERT: E 436 MET cc_start: 0.7875 (ptp) cc_final: 0.7537 (ptm) REVERT: E 561 PHE cc_start: 0.9401 (t80) cc_final: 0.9201 (t80) outliers start: 53 outliers final: 35 residues processed: 165 average time/residue: 0.3464 time to fit residues: 89.4155 Evaluate side-chains 151 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN E 311 HIS E 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21866 Z= 0.186 Angle : 0.611 13.434 29980 Z= 0.315 Chirality : 0.040 0.204 3465 Planarity : 0.004 0.056 3626 Dihedral : 12.627 132.643 3681 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.39 % Favored : 91.49 % Rotamer: Outliers : 2.54 % Allowed : 17.39 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2551 helix: 0.64 (0.17), residues: 964 sheet: -1.05 (0.29), residues: 291 loop : -2.00 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 182 HIS 0.009 0.001 HIS A 75 PHE 0.018 0.001 PHE B 147 TYR 0.016 0.001 TYR D 135 ARG 0.007 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 124 time to evaluate : 2.559 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 370 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8803 (pt0) REVERT: A 566 MET cc_start: 0.9160 (tpp) cc_final: 0.8951 (mmt) REVERT: A 633 MET cc_start: 0.8924 (tmm) cc_final: 0.8595 (tmm) REVERT: A 668 MET cc_start: 0.9441 (tmm) cc_final: 0.9030 (tmm) REVERT: A 855 MET cc_start: 0.8249 (mtm) cc_final: 0.7988 (ptp) REVERT: A 902 MET cc_start: 0.8649 (ttt) cc_final: 0.8167 (tmm) REVERT: A 924 MET cc_start: 0.9565 (mmm) cc_final: 0.9280 (mmm) REVERT: B 49 PHE cc_start: 0.9303 (t80) cc_final: 0.9033 (m-80) REVERT: B 62 MET cc_start: 0.9356 (ppp) cc_final: 0.9022 (ppp) REVERT: B 94 MET cc_start: 0.8317 (ttt) cc_final: 0.8105 (ttt) REVERT: B 142 CYS cc_start: 0.8643 (p) cc_final: 0.8225 (p) REVERT: D 48 GLU cc_start: 0.9167 (pt0) cc_final: 0.8533 (tm-30) REVERT: D 55 MET cc_start: 0.9528 (tmm) cc_final: 0.9133 (tmm) REVERT: D 65 GLN cc_start: 0.9411 (pt0) cc_final: 0.9079 (pp30) REVERT: D 67 MET cc_start: 0.9040 (mtm) cc_final: 0.8726 (mtm) REVERT: D 70 MET cc_start: 0.9390 (tpp) cc_final: 0.8965 (tmm) REVERT: F 68 MET cc_start: 0.8797 (pmm) cc_final: 0.8517 (pmm) REVERT: F 295 LEU cc_start: 0.9804 (OUTLIER) cc_final: 0.9521 (mt) REVERT: F 378 MET cc_start: 0.8877 (tpp) cc_final: 0.8157 (tpp) REVERT: F 474 MET cc_start: 0.7640 (mmt) cc_final: 0.7350 (mmp) REVERT: F 576 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6362 (tmm) REVERT: E 295 LEU cc_start: 0.9810 (tp) cc_final: 0.9495 (pp) REVERT: E 363 LEU cc_start: 0.9579 (mt) cc_final: 0.9162 (mt) REVERT: E 436 MET cc_start: 0.7824 (ptp) cc_final: 0.7491 (ptm) outliers start: 56 outliers final: 34 residues processed: 171 average time/residue: 0.3360 time to fit residues: 90.9452 Evaluate side-chains 151 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21866 Z= 0.231 Angle : 0.635 13.354 29980 Z= 0.326 Chirality : 0.040 0.199 3465 Planarity : 0.004 0.056 3626 Dihedral : 12.589 133.606 3681 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.44 % Rotamer: Outliers : 2.68 % Allowed : 18.25 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2551 helix: 0.64 (0.17), residues: 968 sheet: -0.97 (0.30), residues: 290 loop : -1.95 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.006 0.001 HIS A 892 PHE 0.015 0.001 PHE B 147 TYR 0.016 0.001 TYR A 237 ARG 0.008 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 126 time to evaluate : 2.397 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 380 MET cc_start: 0.8912 (mmm) cc_final: 0.8696 (tpp) REVERT: A 633 MET cc_start: 0.8941 (tmm) cc_final: 0.8590 (tmm) REVERT: A 668 MET cc_start: 0.9434 (tmm) cc_final: 0.9012 (tmm) REVERT: A 855 MET cc_start: 0.8340 (mtm) cc_final: 0.8061 (ptp) REVERT: A 902 MET cc_start: 0.8695 (ttt) cc_final: 0.8229 (tmm) REVERT: A 924 MET cc_start: 0.9551 (mmm) cc_final: 0.9167 (mmm) REVERT: B 49 PHE cc_start: 0.9322 (t80) cc_final: 0.9033 (m-80) REVERT: B 62 MET cc_start: 0.9251 (ppp) cc_final: 0.9004 (ppp) REVERT: D 48 GLU cc_start: 0.9155 (pt0) cc_final: 0.8543 (tm-30) REVERT: D 55 MET cc_start: 0.9531 (tmm) cc_final: 0.9127 (tmm) REVERT: D 65 GLN cc_start: 0.9445 (pt0) cc_final: 0.9108 (pp30) REVERT: D 67 MET cc_start: 0.9065 (mtm) cc_final: 0.8742 (mtm) REVERT: D 70 MET cc_start: 0.9396 (tpp) cc_final: 0.8960 (tmm) REVERT: F 68 MET cc_start: 0.8761 (pmm) cc_final: 0.8484 (pmm) REVERT: F 295 LEU cc_start: 0.9808 (OUTLIER) cc_final: 0.9532 (mt) REVERT: F 378 MET cc_start: 0.8882 (tpp) cc_final: 0.8168 (tpp) REVERT: F 474 MET cc_start: 0.7813 (mmt) cc_final: 0.7598 (mmp) REVERT: F 576 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.6411 (tmm) REVERT: E 363 LEU cc_start: 0.9621 (mt) cc_final: 0.9182 (mt) REVERT: E 436 MET cc_start: 0.7901 (ptp) cc_final: 0.7540 (ptm) outliers start: 59 outliers final: 39 residues processed: 174 average time/residue: 0.3332 time to fit residues: 90.9091 Evaluate side-chains 157 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 47 optimal weight: 0.1980 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 23 optimal weight: 0.0070 chunk 194 optimal weight: 20.0000 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN B 56 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 ASN E 270 GLN E 311 HIS ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21866 Z= 0.149 Angle : 0.611 13.610 29980 Z= 0.310 Chirality : 0.040 0.203 3465 Planarity : 0.004 0.055 3626 Dihedral : 12.491 129.940 3681 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.29 % Favored : 92.59 % Rotamer: Outliers : 1.77 % Allowed : 19.70 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2551 helix: 0.74 (0.17), residues: 970 sheet: -0.60 (0.30), residues: 292 loop : -1.82 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 182 HIS 0.007 0.001 HIS A 892 PHE 0.019 0.001 PHE B 147 TYR 0.009 0.001 TYR A 237 ARG 0.009 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 2.440 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 242 MET cc_start: 0.9180 (mmm) cc_final: 0.8906 (mmm) REVERT: A 370 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8788 (pt0) REVERT: A 380 MET cc_start: 0.8745 (mmm) cc_final: 0.8539 (tpp) REVERT: A 633 MET cc_start: 0.8807 (tmm) cc_final: 0.8530 (tmm) REVERT: A 668 MET cc_start: 0.9397 (tmm) cc_final: 0.9013 (tmm) REVERT: A 902 MET cc_start: 0.8607 (ttt) cc_final: 0.8160 (tmm) REVERT: A 924 MET cc_start: 0.9520 (mmm) cc_final: 0.9113 (mmm) REVERT: B 49 PHE cc_start: 0.9331 (t80) cc_final: 0.9032 (m-80) REVERT: B 62 MET cc_start: 0.9212 (ppp) cc_final: 0.8990 (ppp) REVERT: D 48 GLU cc_start: 0.9181 (pt0) cc_final: 0.8580 (tm-30) REVERT: D 55 MET cc_start: 0.9511 (tmm) cc_final: 0.9118 (tmm) REVERT: D 65 GLN cc_start: 0.9373 (pt0) cc_final: 0.8993 (pp30) REVERT: D 67 MET cc_start: 0.9016 (mtm) cc_final: 0.8620 (mtm) REVERT: D 70 MET cc_start: 0.9372 (tpp) cc_final: 0.8947 (tmm) REVERT: F 68 MET cc_start: 0.8722 (pmm) cc_final: 0.8427 (pmm) REVERT: F 295 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9507 (mt) REVERT: F 378 MET cc_start: 0.8901 (tpp) cc_final: 0.8214 (tpp) REVERT: F 576 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6392 (tmm) REVERT: E 274 MET cc_start: 0.9010 (tpt) cc_final: 0.8799 (tpt) REVERT: E 295 LEU cc_start: 0.9817 (tp) cc_final: 0.9485 (pp) REVERT: E 363 LEU cc_start: 0.9584 (mt) cc_final: 0.9179 (mt) REVERT: E 436 MET cc_start: 0.7873 (ptp) cc_final: 0.7588 (ptm) outliers start: 39 outliers final: 29 residues processed: 168 average time/residue: 0.3616 time to fit residues: 94.2752 Evaluate side-chains 152 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 216 optimal weight: 0.0040 chunk 230 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 70 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 overall best weight: 3.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN A 886 GLN B 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN E 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21866 Z= 0.293 Angle : 0.680 13.327 29980 Z= 0.347 Chirality : 0.041 0.202 3465 Planarity : 0.004 0.054 3626 Dihedral : 12.515 133.750 3681 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.25 % Favored : 90.67 % Rotamer: Outliers : 2.22 % Allowed : 19.93 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2551 helix: 0.62 (0.17), residues: 974 sheet: -0.63 (0.31), residues: 274 loop : -1.89 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.009 0.001 HIS A 75 PHE 0.023 0.001 PHE B 15 TYR 0.018 0.001 TYR A 237 ARG 0.009 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 118 time to evaluate : 2.668 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 633 MET cc_start: 0.8956 (tmm) cc_final: 0.8581 (tmm) REVERT: A 668 MET cc_start: 0.9410 (tmm) cc_final: 0.8977 (tmm) REVERT: A 756 MET cc_start: 0.8478 (ttm) cc_final: 0.8186 (tmm) REVERT: A 902 MET cc_start: 0.8710 (ttt) cc_final: 0.8294 (tmm) REVERT: A 924 MET cc_start: 0.9557 (mmm) cc_final: 0.9122 (mmm) REVERT: B 62 MET cc_start: 0.9355 (ppp) cc_final: 0.9102 (ppp) REVERT: B 82 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8839 (ptpp) REVERT: D 55 MET cc_start: 0.9535 (tmm) cc_final: 0.9114 (tmm) REVERT: D 65 GLN cc_start: 0.9428 (pt0) cc_final: 0.9060 (pp30) REVERT: D 67 MET cc_start: 0.9054 (mtm) cc_final: 0.8711 (mtm) REVERT: D 70 MET cc_start: 0.9415 (tpp) cc_final: 0.8972 (tmm) REVERT: D 90 MET cc_start: 0.9147 (tmm) cc_final: 0.8767 (ppp) REVERT: F 68 MET cc_start: 0.8714 (pmm) cc_final: 0.8415 (pmm) REVERT: F 295 LEU cc_start: 0.9811 (OUTLIER) cc_final: 0.9546 (mt) REVERT: F 378 MET cc_start: 0.8883 (tpp) cc_final: 0.8165 (tpp) REVERT: F 576 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6322 (tmm) REVERT: E 270 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.9050 (mp10) REVERT: E 363 LEU cc_start: 0.9612 (mt) cc_final: 0.9159 (mt) REVERT: E 436 MET cc_start: 0.7896 (ptp) cc_final: 0.7478 (ptm) outliers start: 49 outliers final: 35 residues processed: 158 average time/residue: 0.3783 time to fit residues: 93.6031 Evaluate side-chains 151 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21866 Z= 0.192 Angle : 0.653 14.071 29980 Z= 0.331 Chirality : 0.040 0.201 3465 Planarity : 0.004 0.053 3626 Dihedral : 12.513 131.880 3679 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.08 % Favored : 91.85 % Rotamer: Outliers : 1.72 % Allowed : 20.29 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2551 helix: 0.65 (0.17), residues: 975 sheet: -0.66 (0.31), residues: 281 loop : -1.80 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 167 HIS 0.006 0.001 HIS A 892 PHE 0.017 0.001 PHE B 15 TYR 0.013 0.001 TYR A 237 ARG 0.010 0.000 ARG B 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 2.650 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 633 MET cc_start: 0.8878 (tmm) cc_final: 0.8531 (tmm) REVERT: A 668 MET cc_start: 0.9407 (tmm) cc_final: 0.8998 (tmm) REVERT: A 756 MET cc_start: 0.8477 (ttm) cc_final: 0.8227 (tmm) REVERT: A 902 MET cc_start: 0.8653 (ttt) cc_final: 0.8258 (tmm) REVERT: A 924 MET cc_start: 0.9537 (mmm) cc_final: 0.9094 (mmm) REVERT: B 49 PHE cc_start: 0.8968 (t80) cc_final: 0.8678 (m-80) REVERT: B 62 MET cc_start: 0.9224 (ppp) cc_final: 0.9003 (ppp) REVERT: C 70 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9305 (mtmm) REVERT: D 55 MET cc_start: 0.9527 (tmm) cc_final: 0.9128 (tmm) REVERT: D 65 GLN cc_start: 0.9394 (pt0) cc_final: 0.9016 (pp30) REVERT: D 67 MET cc_start: 0.9042 (mtm) cc_final: 0.8717 (mtm) REVERT: D 70 MET cc_start: 0.9398 (tpp) cc_final: 0.8974 (tmm) REVERT: D 90 MET cc_start: 0.9163 (tmm) cc_final: 0.8732 (ppp) REVERT: F 68 MET cc_start: 0.8689 (pmm) cc_final: 0.8398 (pmm) REVERT: F 295 LEU cc_start: 0.9805 (OUTLIER) cc_final: 0.9512 (mt) REVERT: F 378 MET cc_start: 0.8863 (tpp) cc_final: 0.8160 (tpp) REVERT: F 474 MET cc_start: 0.7155 (tpp) cc_final: 0.6844 (mmp) REVERT: E 363 LEU cc_start: 0.9579 (mt) cc_final: 0.9131 (mt) REVERT: E 436 MET cc_start: 0.7912 (ptp) cc_final: 0.7593 (ptm) REVERT: E 561 PHE cc_start: 0.9373 (t80) cc_final: 0.9162 (t80) outliers start: 38 outliers final: 33 residues processed: 149 average time/residue: 0.3638 time to fit residues: 84.3308 Evaluate side-chains 150 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 116 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN E 311 HIS ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.053891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035926 restraints weight = 143732.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037120 restraints weight = 73760.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037867 restraints weight = 47889.893| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21866 Z= 0.185 Angle : 0.645 14.284 29980 Z= 0.326 Chirality : 0.040 0.206 3465 Planarity : 0.004 0.065 3626 Dihedral : 12.465 131.074 3679 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.47 % Favored : 91.45 % Rotamer: Outliers : 1.86 % Allowed : 20.20 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2551 helix: 0.71 (0.17), residues: 967 sheet: -0.57 (0.31), residues: 271 loop : -1.75 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 167 HIS 0.007 0.001 HIS A 892 PHE 0.021 0.001 PHE B 15 TYR 0.019 0.001 TYR F 180 ARG 0.010 0.000 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4192.22 seconds wall clock time: 78 minutes 20.26 seconds (4700.26 seconds total)