Starting phenix.real_space_refine on Wed May 21 23:41:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gw1_34302/05_2025/8gw1_34302_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gw1_34302/05_2025/8gw1_34302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gw1_34302/05_2025/8gw1_34302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gw1_34302/05_2025/8gw1_34302.map" model { file = "/net/cci-nas-00/data/ceres_data/8gw1_34302/05_2025/8gw1_34302_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gw1_34302/05_2025/8gw1_34302_neut.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 8 6.06 5 P 52 5.49 5 S 157 5.16 5 C 13678 2.51 5 N 3676 2.21 5 O 4270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21843 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7473 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 897} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 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: {'rna3p_pur': 17, '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: "E" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'RNA': 1, 'peptide': 113} Modifications used: {'rna2p_pyr': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106, None: 1} Not linked: pdbres=" U G 0 " pdbres="ASN G 1 " Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 75.304 55.569 122.379 1.00 60.24 S ATOM 2487 SG CYS A 306 75.519 56.910 125.944 1.00 48.09 S ATOM 2519 SG CYS A 310 76.726 53.358 125.081 1.00 48.46 S ATOM 3927 SG CYS A 487 77.876 69.754 106.752 1.00 65.54 S ATOM 5180 SG CYS A 645 77.116 71.762 109.976 1.00 84.84 S ATOM 5186 SG CYS A 646 75.464 68.324 109.350 1.00 90.45 S ATOM 12030 SG CYS E 16 103.395 64.328 51.033 1.00189.89 S ATOM 12045 SG CYS E 19 104.166 60.960 49.289 1.00164.10 S ATOM 11948 SG CYS E 5 115.073 66.319 52.513 1.00156.12 S ATOM 11969 SG CYS E 8 116.595 68.752 50.276 1.00161.33 S ATOM 12107 SG CYS E 26 115.001 70.188 53.045 1.00149.12 S ATOM 12124 SG CYS E 29 112.834 68.396 49.974 1.00160.86 S ATOM 12289 SG CYS E 50 91.629 75.465 62.983 1.00150.56 S ATOM 12319 SG CYS E 55 88.830 74.112 60.779 1.00163.95 S ATOM 12452 SG CYS E 72 90.691 77.367 59.885 1.00156.12 S ATOM 16538 SG CYS F 16 60.494 74.857 67.000 1.00158.14 S ATOM 16553 SG CYS F 19 58.246 71.989 65.639 1.00170.85 S ATOM 16456 SG CYS F 5 69.641 70.707 59.223 1.00166.66 S ATOM 16477 SG CYS F 8 69.616 72.739 56.129 1.00157.20 S ATOM 16615 SG CYS F 26 70.876 74.352 59.097 1.00130.55 S ATOM 16632 SG CYS F 29 67.049 73.701 58.844 1.00154.89 S ATOM 16797 SG CYS F 50 66.543 87.762 81.021 1.00143.10 S ATOM 16827 SG CYS F 55 62.982 88.663 81.857 1.00183.79 S ATOM 16960 SG CYS F 72 64.938 90.764 79.343 1.00174.44 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.74 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.26 residue: pdb=" N AMET F 474 " occ=0.63 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.37 Time building chain proxies: 17.15, per 1000 atoms: 0.79 Number of scatterers: 21843 At special positions: 0 Unit cell: (153.34, 136.94, 185.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Mn 2 24.99 S 157 16.00 P 52 15.00 O 4270 8.00 N 3676 7.00 C 13678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.71 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 28 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 30 sheets defined 41.5% alpha, 14.4% beta 20 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 7.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 4.008A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.779A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.572A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.665A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.737A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.751A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.901A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.993A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.152A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.588A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.618A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.906A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.916A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.692A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.839A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.512A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.584A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.108A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 791 removed outlier: 4.005A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.081A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.960A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 4.447A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.987A pdb=" N THR A 926 " --> pdb=" O ALA A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.625A pdb=" N GLU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 95 removed outlier: 3.581A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.586A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.626A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.917A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.528A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 4.222A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.702A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 80 removed outlier: 4.149A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.580A pdb=" N ALA D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.537A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.711A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.723A pdb=" N LEU D 180 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 72 through 76 removed outlier: 3.946A pdb=" N LYS E 76 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.996A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 removed outlier: 3.611A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 262 through 267 removed outlier: 3.658A pdb=" N ALA E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.796A pdb=" N LEU E 295 " --> pdb=" O PHE E 291 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.616A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 removed outlier: 3.753A pdb=" N TYR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 380 through 391 removed outlier: 3.693A pdb=" N VAL E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN E 388 " --> pdb=" O LEU E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 removed outlier: 3.671A pdb=" N PHE E 422 " --> pdb=" O PRO E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 429 Processing helix chain 'E' and resid 445 through 454 removed outlier: 4.332A pdb=" N THR E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 501 removed outlier: 3.891A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 509 removed outlier: 3.898A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 509 " --> pdb=" O TRP E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 526 removed outlier: 3.764A pdb=" N ASN E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.976A pdb=" N ASN E 557 " --> pdb=" O ALA E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 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 103 through 111 Processing helix chain 'F' and resid 116 through 126 removed outlier: 4.086A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 3.539A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) 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 268 removed outlier: 3.834A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 275 removed outlier: 3.883A pdb=" N VAL F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.878A pdb=" N ALA F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.808A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 329 Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.599A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 422 removed outlier: 3.658A pdb=" N PHE F 422 " --> pdb=" O PRO F 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 419 through 422' Processing helix chain 'F' and resid 423 through 429 removed outlier: 3.857A pdb=" N LEU F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET F 429 " --> pdb=" O VAL F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 454 removed outlier: 3.602A pdb=" N ASP F 450 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 503 removed outlier: 3.648A pdb=" N ARG F 497 " --> pdb=" O ILE F 493 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU F 498 " --> pdb=" O GLY F 494 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG F 502 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN F 503 " --> pdb=" O PHE F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 509 removed outlier: 4.211A pdb=" N LYS F 508 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.869A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 536 No H-bonds generated for 'chain 'F' and resid 534 through 536' Processing helix chain 'F' and resid 561 through 566 Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.332A pdb=" N CYS A 54 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 70 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 114 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.613A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 669 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 189 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757 removed outlier: 3.946A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.910A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.520A pdb=" N LEU D 184 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 149 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.520A pdb=" N LEU D 184 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.515A pdb=" N GLY E 3 " --> pdb=" O THR E 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.683A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 85 removed outlier: 4.069A pdb=" N ALA E 85 " --> pdb=" O GLN E 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 162 through 167 removed outlier: 8.419A pdb=" N GLU E 162 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL E 157 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR E 224 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR E 185 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AB9, first strand: chain 'E' and resid 277 through 279 removed outlier: 6.095A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE E 333 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 530 through 532 removed outlier: 5.933A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP E 542 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY E 571 " --> pdb=" O ASP E 542 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL E 544 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 575 " --> pdb=" O PHE E 546 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N AMET E 474 " --> pdb=" O CYS E 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 480 through 482 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.722A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AC6, first strand: chain 'F' and resid 84 through 85 removed outlier: 4.061A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 162 through 167 removed outlier: 8.490A pdb=" N GLU F 162 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL F 157 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 226 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 347 through 348 removed outlier: 3.533A pdb=" N ARG F 332 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE F 333 " --> pdb=" O THR F 359 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA F 308 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 305 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET F 436 " --> pdb=" O THR F 279 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 281 " --> pdb=" O MET F 436 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'F' and resid 481 through 482 removed outlier: 3.517A pdb=" N THR F 481 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 488 " --> pdb=" O THR F 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 530 through 532 removed outlier: 3.862A pdb=" N THR F 547 " --> pdb=" O ILE F 512 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP F 542 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 544 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.934A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 12.698A pdb=" N SER G 13 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET G 12 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU G 29 " --> pdb=" O MET G 12 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS G 14 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N ASN G 27 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER G 46 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU G 29 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU G 44 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE G 40 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 35 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY G 38 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS G 84 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR G 77 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.25: 3114 1.25 - 1.42: 6486 1.42 - 1.60: 12532 1.60 - 1.77: 52 1.77 - 1.94: 224 Bond restraints: 22408 Sorted by residual: bond pdb=" C ASN G 1 " pdb=" N ASN G 2 " ideal model delta sigma weight residual 1.332 1.684 -0.352 1.40e-02 5.10e+03 6.31e+02 bond pdb=" O5' U G 0 " pdb=" C5' U G 0 " ideal model delta sigma weight residual 1.424 1.074 0.350 1.50e-02 4.44e+03 5.43e+02 bond pdb=" P U G 0 " pdb=" OP1 U G 0 " ideal model delta sigma weight residual 1.485 1.943 -0.458 2.00e-02 2.50e+03 5.25e+02 bond pdb=" C ASN G 2 " pdb=" N GLU G 3 " ideal model delta sigma weight residual 1.330 1.100 0.230 1.31e-02 5.83e+03 3.09e+02 bond pdb=" P U G 0 " pdb=" OP2 U G 0 " ideal model delta sigma weight residual 1.485 1.820 -0.335 2.00e-02 2.50e+03 2.81e+02 ... (remaining 22403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.52: 30650 5.52 - 11.04: 49 11.04 - 16.56: 4 16.56 - 22.09: 3 22.09 - 27.61: 1 Bond angle restraints: 30707 Sorted by residual: angle pdb=" CA ASN G 2 " pdb=" C ASN G 2 " pdb=" N GLU G 3 " ideal model delta sigma weight residual 116.84 89.23 27.61 1.71e+00 3.42e-01 2.61e+02 angle pdb=" N ASN G 1 " pdb=" CA ASN G 1 " pdb=" CB ASN G 1 " ideal model delta sigma weight residual 110.50 92.67 17.83 1.70e+00 3.46e-01 1.10e+02 angle pdb=" N ASN G 2 " pdb=" CA ASN G 2 " pdb=" C ASN G 2 " ideal model delta sigma weight residual 110.80 90.25 20.55 2.13e+00 2.20e-01 9.30e+01 angle pdb=" C ASN G 1 " pdb=" N ASN G 2 " pdb=" CA ASN G 2 " ideal model delta sigma weight residual 121.54 103.91 17.63 1.91e+00 2.74e-01 8.52e+01 angle pdb=" C ASN G 2 " pdb=" N GLU G 3 " pdb=" CA GLU G 3 " ideal model delta sigma weight residual 120.97 104.54 16.43 1.82e+00 3.02e-01 8.15e+01 ... (remaining 30702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.54: 12378 26.54 - 53.08: 942 53.08 - 79.62: 159 79.62 - 106.16: 15 106.16 - 132.70: 1 Dihedral angle restraints: 13495 sinusoidal: 5637 harmonic: 7858 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" CA THR D 84 " pdb=" C THR D 84 " pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" N ASN G 1 " pdb=" C ASN G 1 " pdb=" CA ASN G 1 " pdb=" CB ASN G 1 " ideal model delta harmonic sigma weight residual 122.80 107.92 14.88 0 2.50e+00 1.60e-01 3.54e+01 ... (remaining 13492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.538: 3563 0.538 - 1.077: 0 1.077 - 1.615: 0 1.615 - 2.154: 0 2.154 - 2.692: 1 Chirality restraints: 3564 Sorted by residual: chirality pdb=" P U G 0 " pdb=" OP1 U G 0 " pdb=" OP2 U G 0 " pdb=" O5' U G 0 " both_signs ideal model delta sigma weight residual True 2.41 -5.10 -2.69 2.00e-01 2.50e+01 1.81e+02 chirality pdb=" CA ASN G 1 " pdb=" N ASN G 1 " pdb=" C ASN G 1 " pdb=" CB ASN G 1 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASN G 2 " pdb=" N ASN G 2 " pdb=" C ASN G 2 " pdb=" CB ASN G 2 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3561 not shown) Planarity restraints: 3730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 2 " 0.055 2.00e-02 2.50e+03 1.49e-01 2.22e+02 pdb=" C ASN G 2 " -0.256 2.00e-02 2.50e+03 pdb=" O ASN G 2 " 0.106 2.00e-02 2.50e+03 pdb=" N GLU G 3 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 1 " 0.050 2.00e-02 2.50e+03 9.51e-02 9.04e+01 pdb=" C ASN G 1 " -0.164 2.00e-02 2.50e+03 pdb=" O ASN G 1 " 0.069 2.00e-02 2.50e+03 pdb=" N ASN G 2 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 694 " 0.011 2.00e-02 2.50e+03 1.91e-02 6.39e+00 pdb=" CG PHE A 694 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 694 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 694 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 694 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 694 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 694 " -0.001 2.00e-02 2.50e+03 ... (remaining 3727 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 65 2.35 - 2.99: 11473 2.99 - 3.62: 33629 3.62 - 4.26: 50360 4.26 - 4.90: 82095 Nonbonded interactions: 177622 Sorted by model distance: nonbonded pdb=" P U G 0 " pdb=" N ASN G 1 " model vdw 1.712 3.480 nonbonded pdb=" OD2 ASP A 218 " pdb="MN MN A1004 " model vdw 1.996 2.320 nonbonded pdb=" OD1 ASN A 209 " pdb="MN MN A1004 " model vdw 2.023 2.320 nonbonded pdb=" OG SER A 759 " pdb=" O2' G I 35 " model vdw 2.037 3.040 nonbonded pdb=" ND2 ASN A 209 " pdb="MN MN A1004 " model vdw 2.124 2.400 ... (remaining 177617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 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: 0.980 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 64.170 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.006 0.458 22440 Z= 0.362 Angle : 0.776 27.608 30735 Z= 0.412 Chirality : 0.062 2.692 3564 Planarity : 0.005 0.149 3730 Dihedral : 18.097 132.696 8425 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 0.53 % Allowed : 30.85 % Favored : 68.62 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.16), residues: 2638 helix: -0.26 (0.17), residues: 943 sheet: -1.64 (0.27), residues: 344 loop : -1.99 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.006 0.001 HIS A 82 PHE 0.042 0.002 PHE A 694 TYR 0.020 0.001 TYR A 903 ARG 0.008 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.21463 ( 853) hydrogen bonds : angle 7.68114 ( 2357) metal coordination : bond 0.01984 ( 32) metal coordination : angle 4.83317 ( 28) covalent geometry : bond 0.00638 (22408) covalent geometry : angle 0.76254 (30707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 2.525 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: B 55 MET cc_start: 0.7447 (mmp) cc_final: 0.7069 (mmp) REVERT: B 73 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7673 (tt0) REVERT: F 106 PHE cc_start: 0.7874 (t80) cc_final: 0.7654 (t80) outliers start: 12 outliers final: 2 residues processed: 185 average time/residue: 0.3863 time to fit residues: 106.8537 Evaluate side-chains 170 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 155 optimal weight: 0.2980 chunk 241 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN B 56 GLN B 105 ASN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN E 388 ASN E 559 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN F 354 GLN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.198636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.141489 restraints weight = 79826.825| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 5.15 r_work: 0.3897 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22440 Z= 0.195 Angle : 0.692 11.150 30735 Z= 0.358 Chirality : 0.043 0.230 3564 Planarity : 0.005 0.060 3730 Dihedral : 12.264 129.676 3708 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 3.35 % Allowed : 28.56 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2638 helix: -0.29 (0.17), residues: 972 sheet: -1.66 (0.26), residues: 369 loop : -1.93 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.005 0.001 HIS F 395 PHE 0.024 0.002 PHE E 145 TYR 0.022 0.002 TYR E 71 ARG 0.005 0.000 ARG G 10 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 853) hydrogen bonds : angle 5.80144 ( 2357) metal coordination : bond 0.02142 ( 32) metal coordination : angle 4.80289 ( 28) covalent geometry : bond 0.00440 (22408) covalent geometry : angle 0.67657 (30707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 176 time to evaluate : 2.283 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 40 ASP cc_start: 0.8449 (p0) cc_final: 0.8215 (p0) REVERT: A 63 ASP cc_start: 0.8096 (t0) cc_final: 0.7886 (t0) REVERT: A 116 ARG cc_start: 0.7166 (mtp-110) cc_final: 0.6652 (ttt180) REVERT: B 90 MET cc_start: 0.8886 (tmm) cc_final: 0.8661 (tmm) REVERT: C 13 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8071 (tp) REVERT: D 77 GLU cc_start: 0.8908 (tp30) cc_final: 0.8393 (tm-30) REVERT: F 436 MET cc_start: 0.7161 (pmm) cc_final: 0.6935 (pmm) REVERT: G 32 TYR cc_start: 0.7421 (p90) cc_final: 0.6663 (p90) outliers start: 76 outliers final: 40 residues processed: 235 average time/residue: 0.3504 time to fit residues: 124.8312 Evaluate side-chains 201 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 143 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 142 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 534 ASN E 470 GLN E 562 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.194034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.131128 restraints weight = 74230.739| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 5.49 r_work: 0.3931 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22440 Z= 0.193 Angle : 0.666 12.634 30735 Z= 0.343 Chirality : 0.043 0.230 3564 Planarity : 0.004 0.060 3730 Dihedral : 12.177 130.779 3705 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 4.32 % Allowed : 27.99 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2638 helix: -0.23 (0.17), residues: 976 sheet: -1.64 (0.26), residues: 367 loop : -1.94 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.005 0.001 HIS F 395 PHE 0.017 0.002 PHE D 92 TYR 0.018 0.002 TYR A 788 ARG 0.005 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 853) hydrogen bonds : angle 5.49367 ( 2357) metal coordination : bond 0.01914 ( 32) metal coordination : angle 4.80635 ( 28) covalent geometry : bond 0.00439 (22408) covalent geometry : angle 0.65039 (30707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 175 time to evaluate : 2.333 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 63 ASP cc_start: 0.8164 (t0) cc_final: 0.7949 (t0) REVERT: A 116 ARG cc_start: 0.7128 (mtp-110) cc_final: 0.6606 (ttt180) REVERT: A 372 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 902 MET cc_start: 0.7990 (mmt) cc_final: 0.7773 (mmt) REVERT: B 90 MET cc_start: 0.8850 (tmm) cc_final: 0.8476 (tmm) REVERT: C 13 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8042 (tp) REVERT: E 436 MET cc_start: 0.2508 (mpp) cc_final: 0.1795 (mpp) REVERT: F 130 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9043 (mt) REVERT: F 436 MET cc_start: 0.7098 (pmm) cc_final: 0.6888 (pmm) outliers start: 98 outliers final: 62 residues processed: 254 average time/residue: 0.3482 time to fit residues: 134.8574 Evaluate side-chains 229 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 470 GLN Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN B 56 GLN C 37 ASN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 HIS E 470 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.199930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.143725 restraints weight = 83153.880| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 5.20 r_work: 0.3892 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22440 Z= 0.190 Angle : 0.662 11.859 30735 Z= 0.339 Chirality : 0.043 0.230 3564 Planarity : 0.004 0.061 3730 Dihedral : 12.125 131.219 3705 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 4.41 % Allowed : 28.12 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2638 helix: -0.16 (0.17), residues: 978 sheet: -1.74 (0.26), residues: 347 loop : -1.91 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.005 0.001 HIS F 395 PHE 0.018 0.002 PHE A 102 TYR 0.017 0.002 TYR A 788 ARG 0.005 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 853) hydrogen bonds : angle 5.33660 ( 2357) metal coordination : bond 0.01940 ( 32) metal coordination : angle 5.04993 ( 28) covalent geometry : bond 0.00435 (22408) covalent geometry : angle 0.64455 (30707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 182 time to evaluate : 2.434 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 372 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8411 (mp) REVERT: B 90 MET cc_start: 0.8940 (tmm) cc_final: 0.8526 (tmm) REVERT: C 13 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8110 (tp) REVERT: F 90 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7409 (t80) REVERT: F 436 MET cc_start: 0.7094 (pmm) cc_final: 0.6019 (pmm) REVERT: G 32 TYR cc_start: 0.7514 (p90) cc_final: 0.7121 (p90) REVERT: G 87 TYR cc_start: 0.7417 (m-80) cc_final: 0.7107 (m-80) outliers start: 100 outliers final: 71 residues processed: 266 average time/residue: 0.3691 time to fit residues: 150.9819 Evaluate side-chains 243 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 169 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 209 optimal weight: 10.0000 chunk 230 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 219 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.200951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.141689 restraints weight = 74144.531| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 5.33 r_work: 0.3923 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3928 r_free = 0.3928 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3928 r_free = 0.3928 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22440 Z= 0.129 Angle : 0.616 11.918 30735 Z= 0.315 Chirality : 0.041 0.227 3564 Planarity : 0.004 0.056 3730 Dihedral : 12.036 130.941 3705 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 3.75 % Allowed : 28.96 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2638 helix: 0.06 (0.17), residues: 981 sheet: -1.59 (0.27), residues: 337 loop : -1.82 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS A 82 PHE 0.022 0.001 PHE F 106 TYR 0.012 0.001 TYR F 306 ARG 0.006 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 853) hydrogen bonds : angle 5.06916 ( 2357) metal coordination : bond 0.01680 ( 32) metal coordination : angle 4.48259 ( 28) covalent geometry : bond 0.00283 (22408) covalent geometry : angle 0.60172 (30707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 179 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 643 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8547 (p) REVERT: A 889 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8031 (ttt-90) REVERT: B 90 MET cc_start: 0.8859 (tmm) cc_final: 0.8524 (tmm) REVERT: B 171 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: E 436 MET cc_start: 0.1105 (OUTLIER) cc_final: 0.0262 (mpp) REVERT: F 227 LEU cc_start: -0.0811 (OUTLIER) cc_final: -0.1039 (mt) REVERT: F 436 MET cc_start: 0.7143 (pmm) cc_final: 0.6135 (pmm) REVERT: G 12 MET cc_start: 0.5706 (mpp) cc_final: 0.5487 (mpp) REVERT: G 32 TYR cc_start: 0.7556 (p90) cc_final: 0.7173 (p90) REVERT: G 58 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8230 (ttpp) REVERT: G 87 TYR cc_start: 0.7520 (m-80) cc_final: 0.7259 (m-80) outliers start: 85 outliers final: 55 residues processed: 245 average time/residue: 0.3329 time to fit residues: 126.0107 Evaluate side-chains 225 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 153 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.185434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.132246 restraints weight = 67027.237| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 5.40 r_work: 0.3612 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22440 Z= 0.158 Angle : 0.632 11.524 30735 Z= 0.321 Chirality : 0.041 0.227 3564 Planarity : 0.004 0.059 3730 Dihedral : 11.986 131.522 3705 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 4.23 % Allowed : 28.78 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2638 helix: 0.10 (0.17), residues: 966 sheet: -1.61 (0.26), residues: 355 loop : -1.76 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS E 164 PHE 0.025 0.001 PHE A 694 TYR 0.017 0.001 TYR A 788 ARG 0.006 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 853) hydrogen bonds : angle 5.06668 ( 2357) metal coordination : bond 0.01922 ( 32) metal coordination : angle 4.85491 ( 28) covalent geometry : bond 0.00359 (22408) covalent geometry : angle 0.61493 (30707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 179 time to evaluate : 2.595 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 116 ARG cc_start: 0.7385 (mtp-110) cc_final: 0.6722 (ttt180) REVERT: A 889 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8134 (ttt-90) REVERT: B 90 MET cc_start: 0.8868 (tmm) cc_final: 0.8578 (tmm) REVERT: E 32 ASP cc_start: 0.6920 (m-30) cc_final: 0.5892 (t0) REVERT: F 436 MET cc_start: 0.7109 (pmm) cc_final: 0.6026 (pmm) REVERT: G 12 MET cc_start: 0.5804 (mpp) cc_final: 0.5525 (mpp) REVERT: G 32 TYR cc_start: 0.7363 (p90) cc_final: 0.6884 (p90) REVERT: G 87 TYR cc_start: 0.7402 (m-80) cc_final: 0.7171 (m-80) outliers start: 96 outliers final: 80 residues processed: 259 average time/residue: 0.3469 time to fit residues: 137.2297 Evaluate side-chains 253 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 251 optimal weight: 40.0000 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 0.0770 chunk 207 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.185638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.129042 restraints weight = 91391.364| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 6.57 r_work: 0.3634 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22440 Z= 0.138 Angle : 0.623 11.643 30735 Z= 0.314 Chirality : 0.041 0.226 3564 Planarity : 0.004 0.057 3730 Dihedral : 11.943 131.958 3705 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 4.32 % Allowed : 28.78 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2638 helix: 0.15 (0.17), residues: 981 sheet: -1.48 (0.27), residues: 339 loop : -1.77 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS E 33 PHE 0.024 0.001 PHE F 106 TYR 0.030 0.001 TYR A 903 ARG 0.008 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 853) hydrogen bonds : angle 4.95170 ( 2357) metal coordination : bond 0.01976 ( 32) metal coordination : angle 4.77200 ( 28) covalent geometry : bond 0.00310 (22408) covalent geometry : angle 0.60594 (30707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 177 time to evaluate : 2.479 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 18 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6381 (mmm160) REVERT: A 889 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8209 (ttt-90) REVERT: B 90 MET cc_start: 0.8838 (tmm) cc_final: 0.8552 (tmm) REVERT: B 171 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: D 67 MET cc_start: 0.6473 (tpp) cc_final: 0.6257 (tpt) REVERT: E 32 ASP cc_start: 0.6907 (m-30) cc_final: 0.6003 (t0) REVERT: F 274 MET cc_start: 0.7681 (tmm) cc_final: 0.7419 (tmm) REVERT: F 373 PHE cc_start: 0.8738 (t80) cc_final: 0.8198 (t80) REVERT: F 436 MET cc_start: 0.7009 (pmm) cc_final: 0.5889 (pmm) REVERT: G 12 MET cc_start: 0.5659 (mpp) cc_final: 0.5439 (mpp) REVERT: G 58 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8295 (ttpp) outliers start: 98 outliers final: 77 residues processed: 258 average time/residue: 0.3504 time to fit residues: 139.1567 Evaluate side-chains 249 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 169 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 244 optimal weight: 0.0370 chunk 27 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.186666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.130694 restraints weight = 65927.380| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 5.36 r_work: 0.3630 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22440 Z= 0.135 Angle : 0.618 12.037 30735 Z= 0.311 Chirality : 0.040 0.225 3564 Planarity : 0.004 0.057 3730 Dihedral : 11.895 132.345 3705 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 4.41 % Allowed : 28.78 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2638 helix: 0.26 (0.17), residues: 965 sheet: -1.48 (0.27), residues: 342 loop : -1.70 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS E 164 PHE 0.034 0.001 PHE D 92 TYR 0.015 0.001 TYR A 788 ARG 0.006 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 853) hydrogen bonds : angle 4.87376 ( 2357) metal coordination : bond 0.01757 ( 32) metal coordination : angle 4.72263 ( 28) covalent geometry : bond 0.00305 (22408) covalent geometry : angle 0.60198 (30707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 178 time to evaluate : 2.568 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 18 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6215 (mmm160) REVERT: A 889 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8165 (ttt-90) REVERT: B 90 MET cc_start: 0.8933 (tmm) cc_final: 0.8667 (tmm) REVERT: B 171 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: D 39 LYS cc_start: 0.7169 (pptt) cc_final: 0.6950 (tppt) REVERT: E 32 ASP cc_start: 0.6951 (m-30) cc_final: 0.5997 (t0) REVERT: F 274 MET cc_start: 0.7789 (tmm) cc_final: 0.7536 (tmm) REVERT: F 373 PHE cc_start: 0.8726 (t80) cc_final: 0.8126 (t80) REVERT: F 436 MET cc_start: 0.7148 (pmm) cc_final: 0.6078 (pmm) outliers start: 100 outliers final: 81 residues processed: 261 average time/residue: 0.3452 time to fit residues: 138.9924 Evaluate side-chains 256 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 172 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 233 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 134 optimal weight: 0.0050 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.184046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.129593 restraints weight = 88680.687| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 6.43 r_work: 0.3617 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22440 Z= 0.163 Angle : 0.650 12.076 30735 Z= 0.327 Chirality : 0.042 0.238 3564 Planarity : 0.004 0.063 3730 Dihedral : 11.914 133.189 3705 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 4.19 % Allowed : 29.31 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2638 helix: 0.25 (0.17), residues: 954 sheet: -1.44 (0.27), residues: 331 loop : -1.68 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.010 0.001 HIS E 164 PHE 0.035 0.002 PHE A 694 TYR 0.018 0.001 TYR A 788 ARG 0.008 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 853) hydrogen bonds : angle 4.97255 ( 2357) metal coordination : bond 0.01794 ( 32) metal coordination : angle 4.96667 ( 28) covalent geometry : bond 0.00375 (22408) covalent geometry : angle 0.63317 (30707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 175 time to evaluate : 2.328 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 18 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6324 (mmm160) REVERT: A 116 ARG cc_start: 0.7485 (mtp-110) cc_final: 0.7061 (ttt180) REVERT: A 736 ASP cc_start: 0.7637 (p0) cc_final: 0.7343 (m-30) REVERT: A 889 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8186 (ttt-90) REVERT: B 90 MET cc_start: 0.8883 (tmm) cc_final: 0.8625 (tmm) REVERT: D 39 LYS cc_start: 0.7396 (pptt) cc_final: 0.7173 (tppt) REVERT: E 32 ASP cc_start: 0.6950 (m-30) cc_final: 0.6022 (t0) REVERT: F 274 MET cc_start: 0.7860 (tmm) cc_final: 0.7579 (tmm) REVERT: F 373 PHE cc_start: 0.8775 (t80) cc_final: 0.8166 (t80) REVERT: F 436 MET cc_start: 0.6976 (pmm) cc_final: 0.5820 (pmm) REVERT: G 78 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7095 (m-30) outliers start: 95 outliers final: 81 residues processed: 256 average time/residue: 0.3398 time to fit residues: 133.5466 Evaluate side-chains 255 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 171 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.185646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.129114 restraints weight = 82709.344| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 6.87 r_work: 0.3624 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22440 Z= 0.136 Angle : 0.642 13.920 30735 Z= 0.320 Chirality : 0.041 0.420 3564 Planarity : 0.004 0.056 3730 Dihedral : 11.892 133.415 3705 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 3.79 % Allowed : 29.84 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2638 helix: 0.40 (0.17), residues: 939 sheet: -1.38 (0.27), residues: 343 loop : -1.59 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.010 0.001 HIS E 164 PHE 0.028 0.001 PHE A 694 TYR 0.015 0.001 TYR A 788 ARG 0.009 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 853) hydrogen bonds : angle 4.87713 ( 2357) metal coordination : bond 0.01917 ( 32) metal coordination : angle 4.90094 ( 28) covalent geometry : bond 0.00307 (22408) covalent geometry : angle 0.62516 (30707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 176 time to evaluate : 2.300 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 18 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6368 (mmm160) REVERT: A 736 ASP cc_start: 0.7685 (p0) cc_final: 0.7339 (m-30) REVERT: A 889 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8252 (ttt-90) REVERT: B 77 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7457 (pt0) REVERT: B 90 MET cc_start: 0.8925 (tmm) cc_final: 0.8673 (tmm) REVERT: B 171 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: E 32 ASP cc_start: 0.6874 (m-30) cc_final: 0.6037 (t0) REVERT: F 274 MET cc_start: 0.7883 (tmm) cc_final: 0.7595 (tmm) REVERT: F 373 PHE cc_start: 0.8781 (t80) cc_final: 0.8172 (t80) REVERT: G 78 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: G 89 TYR cc_start: 0.5581 (m-80) cc_final: 0.5194 (m-80) outliers start: 86 outliers final: 77 residues processed: 246 average time/residue: 0.3510 time to fit residues: 132.7156 Evaluate side-chains 250 residues out of total 2318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 169 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 250 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 HIS ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.180068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.123042 restraints weight = 64040.156| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 5.49 r_work: 0.3549 rms_B_bonded: 5.00 restraints_weight: 2.0000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22440 Z= 0.239 Angle : 0.717 12.770 30735 Z= 0.360 Chirality : 0.044 0.250 3564 Planarity : 0.004 0.061 3730 Dihedral : 11.985 135.072 3705 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.10 % Favored : 92.78 % Rotamer: Outliers : 3.92 % Allowed : 29.70 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2638 helix: 0.15 (0.17), residues: 938 sheet: -1.61 (0.26), residues: 367 loop : -1.63 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.010 0.001 HIS E 164 PHE 0.030 0.002 PHE A 694 TYR 0.023 0.002 TYR A 788 ARG 0.009 0.001 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 853) hydrogen bonds : angle 5.16745 ( 2357) metal coordination : bond 0.02042 ( 32) metal coordination : angle 5.44707 ( 28) covalent geometry : bond 0.00558 (22408) covalent geometry : angle 0.69859 (30707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19690.62 seconds wall clock time: 339 minutes 0.31 seconds (20340.31 seconds total)