Starting phenix.real_space_refine on Tue Nov 19 03:41:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/11_2024/6ifu_9657.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/11_2024/6ifu_9657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/11_2024/6ifu_9657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/11_2024/6ifu_9657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/11_2024/6ifu_9657.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifu_9657/11_2024/6ifu_9657.cif" } resolution = 3.05 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 62 5.49 5 S 39 5.16 5 C 11764 2.51 5 N 3178 2.21 5 O 3707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18750 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5561 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 8, 'TRANS': 697} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1690 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2163 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2744 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 606 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 24} Time building chain proxies: 10.45, per 1000 atoms: 0.56 Number of scatterers: 18750 At special positions: 0 Unit cell: (92.56, 135.2, 170.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 62 15.00 O 3707 8.00 N 3178 7.00 C 11764 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: 4.76 Conformation dependent library (CDL) restraints added in 2.1 seconds 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 21 sheets defined 38.9% alpha, 11.0% beta 22 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.504A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.553A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.797A pdb=" N GLY A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.786A pdb=" N ALA A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.728A pdb=" N LEU A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 265 through 291 Processing helix chain 'A' and resid 315 through 335 Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.850A pdb=" N ILE A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 354' Processing helix chain 'A' and resid 359 through 380 removed outlier: 3.901A pdb=" N TYR A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 removed outlier: 3.857A pdb=" N MET A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 432 removed outlier: 4.126A pdb=" N LYS A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.701A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.630A pdb=" N PHE A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.850A pdb=" N GLN A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.511A pdb=" N ALA A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.527A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.637A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 738 through 755 removed outlier: 4.166A pdb=" N LYS A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 36 through 57 removed outlier: 3.830A pdb=" N LEU B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 80 removed outlier: 3.637A pdb=" N LEU B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.568A pdb=" N LYS B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.798A pdb=" N LYS B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 122 removed outlier: 3.649A pdb=" N LEU B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.645A pdb=" N ALA C 13 " --> pdb=" O TYR C 9 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 removed outlier: 3.622A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 62 through 80 removed outlier: 3.924A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.529A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.616A pdb=" N ARG C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 113 " --> pdb=" O CYS C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.710A pdb=" N SER D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 removed outlier: 3.535A pdb=" N VAL D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.919A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.971A pdb=" N LYS E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 163 through 178 removed outlier: 4.129A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.829A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.673A pdb=" N THR E 211 " --> pdb=" O ASP E 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 removed outlier: 3.582A pdb=" N LYS F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 60 " --> pdb=" O MET F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 84 removed outlier: 3.507A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 113 Processing helix chain 'F' and resid 156 through 162 removed outlier: 4.126A pdb=" N GLN F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.660A pdb=" N ILE F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 171 " --> pdb=" O PHE F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 171' Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'G' and resid 29 through 42 removed outlier: 4.042A pdb=" N LYS G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 163 through 177 removed outlier: 3.804A pdb=" N SER G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 230 removed outlier: 4.342A pdb=" N GLU G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 52 removed outlier: 3.646A pdb=" N GLU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.811A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 74 removed outlier: 4.240A pdb=" N ARG H 74 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 82 removed outlier: 3.602A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN H 82 " --> pdb=" O PHE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.548A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 Processing helix chain 'H' and resid 236 through 259 removed outlier: 5.325A pdb=" N GLY H 247 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS H 248 " --> pdb=" O GLU H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 295 Processing helix chain 'H' and resid 296 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 3.701A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 574 removed outlier: 6.815A pdb=" N PHE A 580 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.538A pdb=" N ASP A 519 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 644 through 645 removed outlier: 3.616A pdb=" N PHE A 653 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.303A pdb=" N LYS D 5 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN D 11 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN D 197 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG D 13 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE D 195 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 122 Processing sheet with id=AA9, first strand: chain 'E' and resid 96 through 98 removed outlier: 6.394A pdb=" N LYS E 5 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN E 11 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASN E 197 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG E 13 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE E 195 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 126 Processing sheet with id=AB2, first strand: chain 'F' and resid 96 through 97 removed outlier: 3.585A pdb=" N LEU F 151 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS F 5 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR F 202 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS F 7 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA F 200 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB4, first strand: chain 'G' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'G' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'G' and resid 126 through 132 Processing sheet with id=AB7, first strand: chain 'G' and resid 265 through 266 Processing sheet with id=AB8, first strand: chain 'G' and resid 273 through 274 Processing sheet with id=AB9, first strand: chain 'H' and resid 184 through 186 Processing sheet with id=AC1, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'H' and resid 113 through 115 removed outlier: 6.051A pdb=" N GLU H 113 " --> pdb=" O TYR H 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'H' and resid 212 through 214 639 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3316 1.32 - 1.44: 5302 1.44 - 1.57: 10417 1.57 - 1.69: 125 1.69 - 1.81: 70 Bond restraints: 19230 Sorted by residual: bond pdb=" CB ARG E 136 " pdb=" CG ARG E 136 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.00e+00 bond pdb=" CB VAL A 516 " pdb=" CG2 VAL A 516 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.70e+00 bond pdb=" CG LEU F 18 " pdb=" CD2 LEU F 18 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.18e+00 bond pdb=" CB LEU F 18 " pdb=" CG LEU F 18 " ideal model delta sigma weight residual 1.530 1.477 0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" CB ARG C 65 " pdb=" CG ARG C 65 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 7.02e+00 ... (remaining 19225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 25758 4.33 - 8.66: 420 8.66 - 12.99: 51 12.99 - 17.31: 2 17.31 - 21.64: 1 Bond angle restraints: 26232 Sorted by residual: angle pdb=" N LYS H 146 " pdb=" CA LYS H 146 " pdb=" C LYS H 146 " ideal model delta sigma weight residual 114.62 105.55 9.07 1.14e+00 7.69e-01 6.33e+01 angle pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 103.25 111.40 -8.15 1.05e+00 9.07e-01 6.03e+01 angle pdb=" N PHE A 658 " pdb=" CA PHE A 658 " pdb=" C PHE A 658 " ideal model delta sigma weight residual 110.80 95.79 15.01 2.13e+00 2.20e-01 4.96e+01 angle pdb=" C LEU A 646 " pdb=" N PHE A 647 " pdb=" CA PHE A 647 " ideal model delta sigma weight residual 120.82 130.67 -9.85 1.50e+00 4.44e-01 4.32e+01 angle pdb=" CA LEU H 199 " pdb=" CB LEU H 199 " pdb=" CG LEU H 199 " ideal model delta sigma weight residual 116.30 137.94 -21.64 3.50e+00 8.16e-02 3.82e+01 ... (remaining 26227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 11175 29.39 - 58.78: 352 58.78 - 88.16: 58 88.16 - 117.55: 5 117.55 - 146.94: 4 Dihedral angle restraints: 11594 sinusoidal: 5162 harmonic: 6432 Sorted by residual: dihedral pdb=" CA ASP E 157 " pdb=" C ASP E 157 " pdb=" N GLU E 158 " pdb=" CA GLU E 158 " ideal model delta harmonic sigma weight residual 180.00 -122.67 -57.33 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA SER E 185 " pdb=" C SER E 185 " pdb=" N GLY E 186 " pdb=" CA GLY E 186 " ideal model delta harmonic sigma weight residual 180.00 128.80 51.20 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA VAL F 203 " pdb=" C VAL F 203 " pdb=" N PHE F 204 " pdb=" CA PHE F 204 " ideal model delta harmonic sigma weight residual -180.00 -135.05 -44.95 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 11591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2575 0.106 - 0.211: 353 0.211 - 0.317: 30 0.317 - 0.422: 11 0.422 - 0.528: 3 Chirality restraints: 2972 Sorted by residual: chirality pdb=" CB VAL F 193 " pdb=" CA VAL F 193 " pdb=" CG1 VAL F 193 " pdb=" CG2 VAL F 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB ILE F 12 " pdb=" CA ILE F 12 " pdb=" CG1 ILE F 12 " pdb=" CG2 ILE F 12 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 2969 not shown) Planarity restraints: 3141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.070 2.00e-02 2.50e+03 3.22e-02 2.86e+01 pdb=" N9 A I 27 " -0.076 2.00e-02 2.50e+03 pdb=" C8 A I 27 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 27 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.019 2.00e-02 2.50e+03 pdb=" N1 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.066 2.00e-02 2.50e+03 2.89e-02 2.50e+01 pdb=" N9 G I 21 " -0.069 2.00e-02 2.50e+03 pdb=" C8 G I 21 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G I 21 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G I 21 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.024 2.00e-02 2.50e+03 pdb=" N1 G I 21 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.010 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 19 " -0.052 2.00e-02 2.50e+03 2.74e-02 1.69e+01 pdb=" N1 U I 19 " 0.059 2.00e-02 2.50e+03 pdb=" C2 U I 19 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U I 19 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U I 19 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U I 19 " -0.012 2.00e-02 2.50e+03 pdb=" O4 U I 19 " -0.015 2.00e-02 2.50e+03 pdb=" C5 U I 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 U I 19 " 0.008 2.00e-02 2.50e+03 ... (remaining 3138 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2881 2.75 - 3.28: 17610 3.28 - 3.82: 32700 3.82 - 4.36: 40530 4.36 - 4.90: 67785 Nonbonded interactions: 161506 Sorted by model distance: nonbonded pdb=" OG1 THR D 125 " pdb=" O2 U I 25 " model vdw 2.207 3.040 nonbonded pdb=" O PHE G 71 " pdb=" OH TYR G 157 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR D 16 " pdb=" OD2 ASP H 188 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP G 62 " pdb=" OG SER G 262 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP D 100 " pdb=" NH2 ARG E 140 " model vdw 2.289 3.120 ... (remaining 161501 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' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 66 or resid 76 through 217)) selection = (chain 'E' and (resid 2 through 66 or resid 76 through 217)) selection = (chain 'F' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.470 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.530 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.012 0.127 19230 Z= 0.793 Angle : 1.401 21.643 26232 Z= 0.738 Chirality : 0.076 0.528 2972 Planarity : 0.008 0.056 3141 Dihedral : 14.855 146.940 7446 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.69 % Allowed : 13.89 % Favored : 85.42 % Rotamer: Outliers : 1.42 % Allowed : 7.01 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.99 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.14), residues: 2167 helix: -3.23 (0.12), residues: 798 sheet: -2.87 (0.24), residues: 336 loop : -3.47 (0.15), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.006 TRP A 732 HIS 0.020 0.003 HIS A 695 PHE 0.040 0.005 PHE F 167 TYR 0.037 0.004 TYR A 470 ARG 0.026 0.002 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 544 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.6863 (t) cc_final: 0.6185 (t) REVERT: A 110 ILE cc_start: 0.6679 (mp) cc_final: 0.6353 (mt) REVERT: A 453 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7704 (tp) REVERT: A 633 GLU cc_start: 0.6931 (pp20) cc_final: 0.6694 (pp20) REVERT: C 102 ARG cc_start: 0.8117 (ppp80) cc_final: 0.7772 (ptp-170) REVERT: E 67 LYS cc_start: 0.8237 (ttpm) cc_final: 0.7977 (ttpp) REVERT: E 105 ASN cc_start: 0.8723 (p0) cc_final: 0.8405 (p0) REVERT: E 117 TYR cc_start: 0.8201 (m-80) cc_final: 0.7238 (m-80) REVERT: E 215 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6487 (tm) REVERT: F 11 GLN cc_start: 0.8268 (mm110) cc_final: 0.8054 (mm110) REVERT: F 89 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8166 (pttt) REVERT: F 168 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7523 (mttm) REVERT: F 185 SER cc_start: 0.8492 (p) cc_final: 0.8228 (t) REVERT: H 65 GLN cc_start: 0.7299 (tp-100) cc_final: 0.7008 (tt0) REVERT: H 351 MET cc_start: 0.6853 (pmt) cc_final: 0.6575 (ppp) outliers start: 26 outliers final: 9 residues processed: 559 average time/residue: 0.3802 time to fit residues: 303.5217 Evaluate side-chains 335 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 324 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 158 ASN A 257 ASN A 297 ASN A 312 ASN A 391 ASN A 536 ASN A 562 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN A 699 ASN A 735 ASN C 76 GLN D 134 ASN D 159 ASN E 137 GLN E 197 ASN E 213 ASN F 11 GLN F 134 ASN F 159 ASN F 161 ASN F 197 ASN G 14 HIS G 144 GLN G 273 GLN G 284 HIS H 80 ASN H 82 ASN H 149 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19230 Z= 0.219 Angle : 0.777 14.202 26232 Z= 0.413 Chirality : 0.047 0.365 2972 Planarity : 0.005 0.042 3141 Dihedral : 15.678 152.786 3345 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.72 % Favored : 87.91 % Rotamer: Outliers : 3.56 % Allowed : 13.26 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.47 % 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: -3.73 (0.15), residues: 2167 helix: -1.74 (0.15), residues: 826 sheet: -2.25 (0.26), residues: 335 loop : -3.20 (0.17), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 732 HIS 0.011 0.001 HIS A 695 PHE 0.021 0.002 PHE H 59 TYR 0.017 0.002 TYR A 307 ARG 0.010 0.001 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 679 GLU cc_start: 0.7469 (pm20) cc_final: 0.7114 (pm20) REVERT: C 4 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7853 (pp) REVERT: C 102 ARG cc_start: 0.8181 (ppp80) cc_final: 0.7726 (ttm170) REVERT: E 6 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8137 (pt) REVERT: E 67 LYS cc_start: 0.8184 (ttpm) cc_final: 0.7869 (ttpp) REVERT: E 127 ASP cc_start: 0.7905 (t0) cc_final: 0.7442 (t0) REVERT: E 175 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7542 (ttmt) REVERT: E 215 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6389 (tm) REVERT: F 89 LYS cc_start: 0.8377 (ptpp) cc_final: 0.8143 (pttt) REVERT: F 103 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8517 (tp) REVERT: F 168 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7408 (mttp) REVERT: G 8 MET cc_start: 0.8248 (mtm) cc_final: 0.7493 (mtm) REVERT: G 130 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7721 (m) REVERT: H 65 GLN cc_start: 0.7227 (tp-100) cc_final: 0.6851 (tt0) REVERT: H 241 ARG cc_start: 0.6625 (ptm-80) cc_final: 0.6158 (ptm-80) REVERT: H 351 MET cc_start: 0.6855 (pmt) cc_final: 0.6584 (ppp) outliers start: 65 outliers final: 31 residues processed: 422 average time/residue: 0.3551 time to fit residues: 220.1816 Evaluate side-chains 322 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 218 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 162 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN E 144 ASN E 197 ASN G 104 GLN G 110 ASN G 125 HIS H 148 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19230 Z= 0.227 Angle : 0.727 13.238 26232 Z= 0.387 Chirality : 0.046 0.344 2972 Planarity : 0.004 0.042 3141 Dihedral : 15.341 152.415 3342 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.14 % Favored : 87.54 % Rotamer: Outliers : 3.62 % Allowed : 16.82 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -3.03 (0.16), residues: 2167 helix: -0.92 (0.17), residues: 830 sheet: -1.89 (0.27), residues: 330 loop : -3.03 (0.17), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 732 HIS 0.007 0.001 HIS A 695 PHE 0.019 0.002 PHE G 27 TYR 0.018 0.002 TYR D 181 ARG 0.008 0.001 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 336 time to evaluate : 2.136 Fit side-chains revert: symmetry clash REVERT: A 423 ARG cc_start: 0.6453 (ttp-110) cc_final: 0.6077 (ttp80) REVERT: B 87 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7098 (pp) REVERT: C 4 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7815 (pp) REVERT: D 180 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7363 (t70) REVERT: E 6 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8110 (pt) REVERT: E 14 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8071 (mt) REVERT: E 215 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6478 (tm) REVERT: F 11 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7966 (mm110) REVERT: F 89 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8317 (pttt) REVERT: F 103 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8592 (tp) REVERT: F 168 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7510 (mttm) REVERT: G 130 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7712 (m) REVERT: H 65 GLN cc_start: 0.7311 (tp-100) cc_final: 0.6808 (tt0) REVERT: H 178 ASP cc_start: 0.5290 (p0) cc_final: 0.5022 (t70) REVERT: H 251 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7172 (mt0) REVERT: H 351 MET cc_start: 0.6872 (pmt) cc_final: 0.6600 (ppp) outliers start: 66 outliers final: 33 residues processed: 382 average time/residue: 0.3654 time to fit residues: 206.4012 Evaluate side-chains 333 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9980 chunk 151 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 135 optimal weight: 0.0870 chunk 202 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN B 106 GLN E 33 ASN E 197 ASN G 55 GLN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19230 Z= 0.159 Angle : 0.659 12.428 26232 Z= 0.350 Chirality : 0.043 0.343 2972 Planarity : 0.004 0.062 3141 Dihedral : 15.123 153.381 3338 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.72 % Favored : 88.09 % Rotamer: Outliers : 3.84 % Allowed : 16.82 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.17), residues: 2167 helix: -0.33 (0.18), residues: 820 sheet: -1.68 (0.27), residues: 330 loop : -2.81 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 PHE 0.019 0.001 PHE G 27 TYR 0.019 0.001 TYR B 68 ARG 0.009 0.001 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4334 Ramachandran restraints generated. 2167 Oldfield, 0 Emsley, 2167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 344 time to evaluate : 1.969 Fit side-chains REVERT: A 29 LYS cc_start: 0.7396 (mptt) cc_final: 0.6975 (ptmt) REVERT: A 177 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7300 (t80) REVERT: A 423 ARG cc_start: 0.6501 (ttp-110) cc_final: 0.6148 (ttp80) REVERT: A 679 GLU cc_start: 0.7466 (pm20) cc_final: 0.7141 (pm20) REVERT: B 18 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7933 (mm) REVERT: B 87 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7072 (pp) REVERT: C 4 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7558 (pp) REVERT: E 6 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7868 (pt) REVERT: E 11 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: E 14 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7898 (mt) REVERT: E 215 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6434 (tm) REVERT: F 103 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8570 (tp) REVERT: F 168 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7523 (mttm) REVERT: G 8 MET cc_start: 0.8346 (mtm) cc_final: 0.7907 (mtm) REVERT: G 130 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7612 (m) REVERT: H 65 GLN cc_start: 0.7234 (tp-100) cc_final: 0.6908 (tt0) REVERT: H 199 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8531 (pp) REVERT: H 251 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7128 (mt0) outliers start: 70 outliers final: 33 residues processed: 392 average time/residue: 0.3494 time to fit residues: 201.7144 Evaluate side-chains 334 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 157 TYR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 0.3980 chunk 121 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN D 144 ASN E 197 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4080 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: