Starting phenix.real_space_refine on Sun Sep 13 08:21:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xn3_22266/09_2026/6xn3_22266.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 1.543 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 70 5.49 5 S 52 5.16 5 C 13784 2.51 5 N 3747 2.21 5 O 4396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22049 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5984 Classifications: {'peptide': 741} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 730} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2232 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 276, 2230 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 276, 2230 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2277 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2467 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 286} Chain breaks: 3 Chain: "R" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 6, 'rna3p_pur': 5, 'rna3p_pyr': 14} Link IDs: {'rna2p': 18, 'rna3p': 18} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "E" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Chain: "T" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 734 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 27} Time building chain proxies: 4.97, per 1000 atoms: 0.23 Number of scatterers: 22049 At special positions: 0 Unit cell: (122.436, 126.732, 208.356, 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 52 16.00 P 70 15.00 O 4396 8.00 N 3747 7.00 C 13784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.01 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 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: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 30 sheets defined 44.4% alpha, 14.5% beta 16 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 28 through 38 removed outlier: 3.858A pdb=" N LEU A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.732A pdb=" N THR A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.527A pdb=" N ASN A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.674A pdb=" N LYS A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.550A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 202 through 225 removed outlier: 3.507A pdb=" N HIS A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 268 through 295 removed outlier: 3.510A pdb=" N LEU A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 317 through 339 Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.514A pdb=" N ASN A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 418 through 430 removed outlier: 4.383A pdb=" N GLN A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.932A pdb=" N LEU A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.890A pdb=" N VAL A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 removed outlier: 3.744A pdb=" N ALA A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.808A pdb=" N THR A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.110A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.807A pdb=" N LYS A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 684 " --> pdb=" O ASN A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 702 Processing helix chain 'A' and resid 705 through 720 removed outlier: 3.848A pdb=" N ASN A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 710 " --> pdb=" O GLN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 removed outlier: 3.513A pdb=" N GLY A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 removed outlier: 3.632A pdb=" N ALA A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 755 removed outlier: 4.051A pdb=" N LEU A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 744 " --> pdb=" O ARG A 740 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.504A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.717A pdb=" N ASN B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.802A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 74 through 82 Processing helix chain 'F' and resid 103 through 110 Processing helix chain 'F' and resid 157 through 174 removed outlier: 3.754A pdb=" N PHE F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 Processing helix chain 'F' and resid 204 through 213 removed outlier: 3.803A pdb=" N LEU F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.854A pdb=" N ASP H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 157 through 173 Processing helix chain 'H' and resid 205 through 213 removed outlier: 3.631A pdb=" N ILE H 211 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.577A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 154 through 156 No H-bonds generated for 'chain 'G' and resid 154 through 156' Processing helix chain 'G' and resid 157 through 174 removed outlier: 3.901A pdb=" N PHE G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 removed outlier: 4.205A pdb=" N LEU G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.538A pdb=" N LEU I 49 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.867A pdb=" N ASP I 73 " --> pdb=" O PRO I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 103 through 111 Processing helix chain 'I' and resid 157 through 172 Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.705A pdb=" N GLU I 210 " --> pdb=" O ASN I 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 51 Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 127 through 140 removed outlier: 3.744A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 154 No H-bonds generated for 'chain 'J' and resid 152 through 154' Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 228 Processing helix chain 'J' and resid 228 through 235 Processing helix chain 'J' and resid 238 through 242 removed outlier: 3.912A pdb=" N GLY J 241 " --> pdb=" O LEU J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 286 through 300 removed outlier: 4.152A pdb=" N GLN J 290 " --> pdb=" O LYS J 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA J 291 " --> pdb=" O ASN J 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.721A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 Processing helix chain 'D' and resid 53 through 69 removed outlier: 3.813A pdb=" N ILE D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.621A pdb=" N GLU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 112 through 123 removed outlier: 3.660A pdb=" N ALA D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.701A pdb=" N PHE D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 39 removed outlier: 3.505A pdb=" N HIS E 39 " --> pdb=" O ARG E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 removed outlier: 4.007A pdb=" N ARG E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.534A pdb=" N GLU E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 111 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 125 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 255 removed outlier: 4.060A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.656A pdb=" N TYR A 304 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.522A pdb=" N GLN A 472 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 568 through 572 removed outlier: 7.035A pdb=" N PHE A 579 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 653 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 removed outlier: 11.721A pdb=" N ALA B 62 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE B 59 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU B 160 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP B 61 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 158 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 65 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR B 153 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE B 8 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 159 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 132 removed outlier: 3.629A pdb=" N THR B 148 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 185 removed outlier: 4.495A pdb=" N GLY B 185 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN F 97 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU F 147 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.573A pdb=" N ASP B 272 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 84 removed outlier: 3.807A pdb=" N ARG F 90 " --> pdb=" O SER F 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AB6, first strand: chain 'H' and resid 94 through 95 removed outlier: 4.553A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 35 through 36 removed outlier: 3.699A pdb=" N LEU H 41 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AB9, first strand: chain 'G' and resid 43 through 44 removed outlier: 4.663A pdb=" N LYS G 100 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 145 " --> pdb=" O LYS G 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 43 through 44 removed outlier: 4.663A pdb=" N LYS G 100 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP G 145 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR G 8 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN G 192 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL G 10 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE G 190 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AC3, first strand: chain 'I' and resid 143 through 151 Processing sheet with id=AC4, first strand: chain 'I' and resid 143 through 151 Processing sheet with id=AC5, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'I' and resid 115 through 120 Processing sheet with id=AC7, first strand: chain 'J' and resid 156 through 158 removed outlier: 3.597A pdb=" N THR J 195 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 22 through 23 removed outlier: 7.422A pdb=" N ASN J 114 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N LEU J 191 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG J 188 " --> pdb=" O TYR J 172 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 29 through 31 removed outlier: 3.770A pdb=" N MET J 39 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR J 86 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AD2, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AD3, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.704A pdb=" N PHE D 42 " --> pdb=" O GLN D 50 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7048 1.35 - 1.49: 6169 1.49 - 1.63: 9257 1.63 - 1.77: 9 1.77 - 1.91: 88 Bond restraints: 22571 Sorted by residual: bond pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 1.808 1.908 -0.100 3.30e-02 9.18e+02 9.16e+00 bond pdb=" CG1 ILE D 140 " pdb=" CD1 ILE D 140 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.71e+00 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.89e+00 bond pdb=" CG1 ILE A 213 " pdb=" CD1 ILE A 213 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.51e+00 bond pdb=" N GLU A 414 " pdb=" CA GLU A 414 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.16e+00 ... (remaining 22566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 30261 3.98 - 7.95: 421 7.95 - 11.93: 38 11.93 - 15.91: 4 15.91 - 19.88: 1 Bond angle restraints: 30725 Sorted by residual: angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 121.70 137.58 -15.88 1.80e+00 3.09e-01 7.79e+01 angle pdb=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.28 -19.88 2.30e+00 1.89e-01 7.47e+01 angle pdb=" C3' A R 33 " pdb=" O3' A R 33 " pdb=" P C R 34 " ideal model delta sigma weight residual 119.70 128.84 -9.14 1.20e+00 6.94e-01 5.80e+01 angle pdb=" C3' A R 32 " pdb=" O3' A R 32 " pdb=" P A R 33 " ideal model delta sigma weight residual 119.70 128.12 -8.42 1.20e+00 6.94e-01 4.92e+01 angle pdb=" N GLY B 185 " pdb=" CA GLY B 185 " pdb=" C GLY B 185 " ideal model delta sigma weight residual 113.18 98.14 15.04 2.37e+00 1.78e-01 4.03e+01 ... (remaining 30720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 13067 34.00 - 68.00: 372 68.00 - 102.00: 49 102.00 - 136.00: 1 136.00 - 170.00: 2 Dihedral angle restraints: 13491 sinusoidal: 6029 harmonic: 7462 Sorted by residual: dihedral pdb=" C4' A R 21 " pdb=" C3' A R 21 " pdb=" C2' A R 21 " pdb=" C1' A R 21 " ideal model delta sinusoidal sigma weight residual 36.35 -39.13 75.47 1 3.10e+00 1.04e-01 7.48e+02 dihedral pdb=" C4' A R 32 " pdb=" C3' A R 32 " pdb=" C2' A R 32 " pdb=" C1' A R 32 " ideal model delta sinusoidal sigma weight residual 36.35 -38.25 74.60 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' U R 14 " pdb=" C3' U R 14 " pdb=" C2' U R 14 " pdb=" C1' U R 14 " ideal model delta sinusoidal sigma weight residual 36.34 -37.83 74.18 1 3.10e+00 1.04e-01 7.27e+02 ... (remaining 13488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2836 0.082 - 0.163: 471 0.163 - 0.245: 136 0.245 - 0.326: 40 0.326 - 0.408: 12 Chirality restraints: 3495 Sorted by residual: chirality pdb=" C2' A R 32 " pdb=" C3' A R 32 " pdb=" O2' A R 32 " pdb=" C1' A R 32 " both_signs ideal model delta sigma weight residual False -2.79 -2.38 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C1' A R 21 " pdb=" O4' A R 21 " pdb=" C2' A R 21 " pdb=" N9 A R 21 " both_signs ideal model delta sigma weight residual False 2.46 2.06 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C1' A R 25 " pdb=" O4' A R 25 " pdb=" C2' A R 25 " pdb=" N9 A R 25 " both_signs ideal model delta sigma weight residual False 2.46 2.06 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 3492 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 169 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 170 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 553 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C PHE A 553 " 0.066 2.00e-02 2.50e+03 pdb=" O PHE A 553 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS A 554 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 306 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C THR J 306 " 0.054 2.00e-02 2.50e+03 pdb=" O THR J 306 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR J 307 " -0.018 2.00e-02 2.50e+03 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2955 2.75 - 3.29: 20705 3.29 - 3.82: 37481 3.82 - 4.36: 43997 4.36 - 4.90: 75115 Nonbonded interactions: 180253 Sorted by model distance: nonbonded pdb=" OG SER J 295 " pdb=" OG1 THR J 306 " model vdw 2.211 3.040 nonbonded pdb=" O ILE I 26 " pdb=" O2' U T 11 " model vdw 2.254 3.040 nonbonded pdb=" O THR E 125 " pdb=" OG SER E 128 " model vdw 2.263 3.040 nonbonded pdb=" O PHE C 107 " pdb=" OG1 THR C 111 " model vdw 2.272 3.040 nonbonded pdb=" O THR A 317 " pdb=" OG1 THR A 320 " model vdw 2.276 3.040 ... (remaining 180248 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 'C' and (resid 16 through 43 or resid 50 through 146)) selection = (chain 'D' and (resid 16 through 43 or resid 50 through 146)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 65 or resid 73 through 214)) } 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=0.50 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: 1.110 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.570 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.008 0.108 22574 Z= 0.338 Angle : 1.197 19.884 30731 Z= 0.635 Chirality : 0.077 0.408 3495 Planarity : 0.006 0.119 3683 Dihedral : 16.051 170.000 8676 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.04 % Allowed : 0.81 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.14), residues: 2530 helix: -1.85 (0.13), residues: 1048 sheet: -1.60 (0.26), residues: 352 loop : -2.64 (0.15), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG I 183 TYR 0.039 0.003 TYR I 176 PHE 0.049 0.003 PHE G 162 TRP 0.020 0.003 TRP A 186 HIS 0.013 0.002 HIS G 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.34 (22571) covalent geometry : angle 1.19082 / 0.63 (30725) SS BOND : bond 0.01894 / 0.92 ( 3) SS BOND : angle 8.75173 / 4.10 ( 6) hydrogen bonds : bond 0.17840 / 11.50 ( 961) hydrogen bonds : angle 7.97083 / 5.43 ( 2776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 517 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.5263 (pmm) cc_final: 0.5019 (pmm) REVERT: A 230 GLN cc_start: 0.5940 (pp30) cc_final: 0.5612 (pp30) REVERT: A 285 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 488 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.7019 (ttm-80) REVERT: A 545 PHE cc_start: 0.7309 (t80) cc_final: 0.6865 (t80) REVERT: A 558 ASN cc_start: 0.7306 (m110) cc_final: 0.6749 (m110) REVERT: A 637 ASP cc_start: 0.7442 (m-30) cc_final: 0.7159 (m-30) REVERT: J 22 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8154 (ptmm) REVERT: D 97 GLU cc_start: 0.7577 (tt0) cc_final: 0.7366 (tt0) outliers start: 1 outliers final: 1 residues processed: 517 average time/residue: 0.5493 time to fit residues: 330.3905 Evaluate side-chains 381 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN I 209 ASN J 114 ASN J 157 GLN J 287 ASN J 290 GLN C 25 ASN C 109 GLN C 122 ASN D 69 ASN D 109 GLN E 18 ASN E 69 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122822 restraints weight = 42894.861| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.94 r_work: 0.3439 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22574 Z= 0.212 Angle : 0.963 27.476 30731 Z= 0.451 Chirality : 0.087 1.662 3495 Planarity : 0.005 0.090 3683 Dihedral : 12.459 178.115 3627 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.11 % Allowed : 14.04 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 2530 helix: -0.58 (0.15), residues: 1058 sheet: -1.59 (0.25), residues: 387 loop : -2.50 (0.16), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 35 TYR 0.019 0.002 TYR E 89 PHE 0.033 0.002 PHE J 30 TRP 0.014 0.002 TRP A 186 HIS 0.006 0.001 HIS G 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (22571) covalent geometry : angle 0.95537 / 0.45 (30725) SS BOND : bond 0.01761 / 0.86 ( 3) SS BOND : angle 8.61325 / 4.06 ( 6) hydrogen bonds : bond 0.04805 / 3.17 ( 961) hydrogen bonds : angle 5.58956 / 3.87 ( 2776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 452 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4946 (ttp) cc_final: 0.4582 (tpp) REVERT: A 173 GLU cc_start: 0.7304 (pp20) cc_final: 0.6950 (pp20) REVERT: A 230 GLN cc_start: 0.6074 (pp30) cc_final: 0.5730 (pp30) REVERT: A 253 ASP cc_start: 0.8826 (t0) cc_final: 0.8422 (t0) REVERT: A 283 LEU cc_start: 0.8946 (mt) cc_final: 0.8636 (mt) REVERT: A 285 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8178 (tp30) REVERT: A 358 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.5296 (tmm) REVERT: A 486 MET cc_start: 0.4845 (mtp) cc_final: 0.4011 (mpp) REVERT: A 488 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.7119 (ttm-80) REVERT: A 494 TYR cc_start: 0.8150 (t80) cc_final: 0.7940 (t80) REVERT: A 545 PHE cc_start: 0.7806 (t80) cc_final: 0.7390 (t80) REVERT: A 558 ASN cc_start: 0.8096 (m110) cc_final: 0.7224 (m110) REVERT: A 637 ASP cc_start: 0.8108 (m-30) cc_final: 0.7802 (m-30) REVERT: A 713 LEU cc_start: 0.9046 (tp) cc_final: 0.8811 (tp) REVERT: A 726 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7625 (mmtp) REVERT: B 21 GLU cc_start: 0.7802 (pp20) cc_final: 0.7577 (pp20) REVERT: B 232 TYR cc_start: 0.8204 (p90) cc_final: 0.7764 (p90) REVERT: B 274 TYR cc_start: 0.8647 (m-80) cc_final: 0.8357 (m-80) REVERT: F 154 ASP cc_start: 0.8282 (t0) cc_final: 0.8020 (t70) REVERT: I 15 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8015 (tmm) REVERT: I 93 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7765 (mtp85) REVERT: I 134 GLN cc_start: 0.8604 (mp-120) cc_final: 0.8296 (mt0) REVERT: I 209 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7877 (m110) REVERT: J 21 GLU cc_start: 0.7445 (tp30) cc_final: 0.6884 (tp30) REVERT: J 119 ASP cc_start: 0.8457 (p0) cc_final: 0.8226 (p0) REVERT: J 157 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: J 188 ARG cc_start: 0.8495 (ptp-170) cc_final: 0.8162 (mtt180) REVERT: C 97 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 118 THR cc_start: 0.8642 (p) cc_final: 0.8277 (p) REVERT: C 122 ASN cc_start: 0.8997 (m-40) cc_final: 0.8685 (m110) REVERT: D 97 GLU cc_start: 0.8549 (tt0) cc_final: 0.8054 (tt0) REVERT: E 22 ASN cc_start: 0.8479 (m-40) cc_final: 0.8074 (p0) REVERT: E 34 ILE cc_start: 0.8981 (mm) cc_final: 0.8687 (mp) REVERT: E 70 ARG cc_start: 0.8824 (ttt-90) cc_final: 0.8610 (ttt-90) outliers start: 47 outliers final: 16 residues processed: 467 average time/residue: 0.5188 time to fit residues: 284.3688 Evaluate side-chains 409 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 387 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 93 ARG Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN G 63 ASN I 209 ASN J 290 GLN C 123 GLN D 69 ASN D 73 ASN D 109 GLN E 25 ASN E 50 GLN E 69 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126470 restraints weight = 48111.238| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.21 r_work: 0.3453 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22574 Z= 0.159 Angle : 0.804 17.136 30731 Z= 0.384 Chirality : 0.071 1.463 3495 Planarity : 0.004 0.051 3683 Dihedral : 12.384 176.279 3626 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.42 % Allowed : 16.87 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.15), residues: 2530 helix: -0.05 (0.15), residues: 1063 sheet: -1.52 (0.25), residues: 375 loop : -2.38 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 35 TYR 0.020 0.001 TYR A 218 PHE 0.015 0.001 PHE A 73 TRP 0.008 0.001 TRP J 228 HIS 0.004 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (22571) covalent geometry : angle 0.79520 / 0.38 (30725) SS BOND : bond 0.01836 / 0.90 ( 3) SS BOND : angle 8.52675 / 4.02 ( 6) hydrogen bonds : bond 0.04132 / 2.71 ( 961) hydrogen bonds : angle 5.10509 / 3.53 ( 2776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 440 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4677 (ttp) cc_final: 0.4326 (tpp) REVERT: A 86 MET cc_start: 0.4130 (pmm) cc_final: 0.3905 (pmm) REVERT: A 173 GLU cc_start: 0.6721 (pp20) cc_final: 0.6418 (pp20) REVERT: A 230 GLN cc_start: 0.6057 (pp30) cc_final: 0.5817 (pp30) REVERT: A 253 ASP cc_start: 0.8871 (t0) cc_final: 0.8325 (t0) REVERT: A 282 MET cc_start: 0.8493 (tpp) cc_final: 0.8155 (tpp) REVERT: A 285 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8285 (tp30) REVERT: A 332 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8343 (tttt) REVERT: A 453 MET cc_start: 0.7883 (ttp) cc_final: 0.7441 (mtp) REVERT: A 464 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4813 (tm) REVERT: A 558 ASN cc_start: 0.8074 (m110) cc_final: 0.7220 (m110) REVERT: A 637 ASP cc_start: 0.8170 (m-30) cc_final: 0.7862 (m-30) REVERT: A 671 PHE cc_start: 0.7780 (m-10) cc_final: 0.7572 (m-10) REVERT: A 720 MET cc_start: 0.8243 (mtp) cc_final: 0.7949 (mtp) REVERT: A 726 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7609 (mmtp) REVERT: B 21 GLU cc_start: 0.7815 (pp20) cc_final: 0.7524 (pp20) REVERT: B 209 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8098 (ttm-80) REVERT: B 232 TYR cc_start: 0.8436 (p90) cc_final: 0.7707 (p90) REVERT: F 120 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: F 183 ARG cc_start: 0.8514 (mpp80) cc_final: 0.8289 (mtm110) REVERT: G 6 GLU cc_start: 0.8521 (tt0) cc_final: 0.8286 (mt-10) REVERT: I 15 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8125 (tmm) REVERT: I 93 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7735 (mtp85) REVERT: I 134 GLN cc_start: 0.8659 (mp-120) cc_final: 0.8323 (mt0) REVERT: J 21 GLU cc_start: 0.7586 (tp30) cc_final: 0.6910 (tp30) REVERT: J 47 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7469 (pptt) REVERT: J 119 ASP cc_start: 0.8496 (p0) cc_final: 0.8235 (p0) REVERT: J 204 ASP cc_start: 0.7454 (m-30) cc_final: 0.6363 (p0) REVERT: J 227 LYS cc_start: 0.7075 (tptt) cc_final: 0.6858 (tptt) REVERT: C 44 ASN cc_start: 0.8020 (p0) cc_final: 0.7670 (p0) REVERT: C 118 THR cc_start: 0.8711 (p) cc_final: 0.8183 (p) REVERT: C 122 ASN cc_start: 0.8901 (m-40) cc_final: 0.8381 (m110) REVERT: C 127 GLU cc_start: 0.8806 (mp0) cc_final: 0.8589 (tp30) REVERT: D 97 GLU cc_start: 0.8627 (tt0) cc_final: 0.8023 (tt0) REVERT: E 34 ILE cc_start: 0.8814 (mm) cc_final: 0.8503 (mp) outliers start: 76 outliers final: 25 residues processed: 468 average time/residue: 0.4814 time to fit residues: 267.0454 Evaluate side-chains 426 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 396 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 93 ARG Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 123 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 109 GLN E 50 GLN E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125920 restraints weight = 50706.056| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.18 r_work: 0.3449 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22574 Z= 0.162 Angle : 0.781 16.677 30731 Z= 0.373 Chirality : 0.070 1.495 3495 Planarity : 0.004 0.060 3683 Dihedral : 12.351 175.104 3626 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.69 % Allowed : 19.48 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2530 helix: 0.26 (0.16), residues: 1069 sheet: -1.44 (0.25), residues: 392 loop : -2.35 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 183 TYR 0.022 0.001 TYR A 218 PHE 0.015 0.001 PHE C 129 TRP 0.010 0.001 TRP A 663 HIS 0.004 0.001 HIS G 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (22571) covalent geometry : angle 0.77151 / 0.37 (30725) SS BOND : bond 0.01947 / 0.95 ( 3) SS BOND : angle 8.61953 / 4.12 ( 6) hydrogen bonds : bond 0.04012 / 2.64 ( 961) hydrogen bonds : angle 4.88566 / 3.38 ( 2776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 442 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4940 (ttp) cc_final: 0.4396 (tpp) REVERT: A 173 GLU cc_start: 0.6851 (pp20) cc_final: 0.6561 (pp20) REVERT: A 181 MET cc_start: 0.2914 (mmp) cc_final: 0.2640 (mmt) REVERT: A 230 GLN cc_start: 0.5966 (pp30) cc_final: 0.5727 (pp30) REVERT: A 253 ASP cc_start: 0.8922 (t0) cc_final: 0.8299 (t0) REVERT: A 358 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.5202 (tmm) REVERT: A 464 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.4913 (tm) REVERT: A 558 ASN cc_start: 0.8126 (m110) cc_final: 0.7275 (m110) REVERT: A 612 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8544 (mm) REVERT: A 637 ASP cc_start: 0.8179 (m-30) cc_final: 0.7863 (m-30) REVERT: A 720 MET cc_start: 0.8155 (mtp) cc_final: 0.7842 (mtp) REVERT: A 726 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7616 (mmtt) REVERT: B 209 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8178 (ttm-80) REVERT: B 232 TYR cc_start: 0.8483 (p90) cc_final: 0.7710 (p90) REVERT: F 120 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: F 154 ASP cc_start: 0.8066 (t70) cc_final: 0.7822 (t0) REVERT: F 156 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8110 (tppp) REVERT: H 15 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7861 (tmm) REVERT: H 74 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: G 6 GLU cc_start: 0.8456 (tt0) cc_final: 0.8191 (mt-10) REVERT: I 15 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8048 (tmm) REVERT: I 93 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7666 (mtp85) REVERT: I 134 GLN cc_start: 0.8704 (mp-120) cc_final: 0.8408 (mt0) REVERT: I 150 TYR cc_start: 0.8971 (t80) cc_final: 0.8746 (t80) REVERT: I 151 ASN cc_start: 0.8259 (t0) cc_final: 0.7604 (t0) REVERT: J 21 GLU cc_start: 0.7593 (tp30) cc_final: 0.6850 (tp30) REVERT: J 47 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7436 (pptt) REVERT: J 119 ASP cc_start: 0.8525 (p0) cc_final: 0.8242 (p0) REVERT: J 188 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.8311 (ptt180) REVERT: C 44 ASN cc_start: 0.8071 (p0) cc_final: 0.7707 (p0) REVERT: C 118 THR cc_start: 0.8782 (p) cc_final: 0.8184 (p) REVERT: C 122 ASN cc_start: 0.8919 (m-40) cc_final: 0.8439 (m110) REVERT: C 127 GLU cc_start: 0.8844 (mp0) cc_final: 0.8590 (tp30) REVERT: D 19 GLU cc_start: 0.7455 (pm20) cc_final: 0.7128 (pm20) REVERT: D 97 GLU cc_start: 0.8628 (tt0) cc_final: 0.8229 (tt0) REVERT: E 34 ILE cc_start: 0.8757 (mm) cc_final: 0.8453 (mp) REVERT: E 105 LYS cc_start: 0.7686 (ttmm) cc_final: 0.7268 (mtpt) REVERT: E 129 PHE cc_start: 0.8588 (t80) cc_final: 0.8210 (t80) outliers start: 82 outliers final: 37 residues processed: 483 average time/residue: 0.4852 time to fit residues: 277.6847 Evaluate side-chains 432 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 386 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 93 ARG Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 216 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 251 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 145 optimal weight: 0.0770 chunk 223 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 709 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 109 GLN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123856 restraints weight = 39730.717| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.79 r_work: 0.3460 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22574 Z= 0.170 Angle : 0.786 16.784 30731 Z= 0.376 Chirality : 0.070 1.502 3495 Planarity : 0.004 0.063 3683 Dihedral : 12.369 178.534 3626 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.51 % Allowed : 21.64 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2530 helix: 0.42 (0.16), residues: 1070 sheet: -1.37 (0.25), residues: 391 loop : -2.32 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 183 TYR 0.016 0.001 TYR E 89 PHE 0.015 0.001 PHE A 73 TRP 0.006 0.001 TRP A 663 HIS 0.004 0.001 HIS G 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (22571) covalent geometry : angle 0.77630 / 0.37 (30725) SS BOND : bond 0.01995 / 0.98 ( 3) SS BOND : angle 8.61806 / 4.13 ( 6) hydrogen bonds : bond 0.03954 / 2.60 ( 961) hydrogen bonds : angle 4.85669 / 3.36 ( 2776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 420 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4967 (ttp) cc_final: 0.4635 (tpp) REVERT: A 173 GLU cc_start: 0.6771 (pp20) cc_final: 0.6510 (pp20) REVERT: A 181 MET cc_start: 0.2853 (mmp) cc_final: 0.2611 (mmt) REVERT: A 230 GLN cc_start: 0.5991 (pp30) cc_final: 0.5725 (pp30) REVERT: A 253 ASP cc_start: 0.8869 (t0) cc_final: 0.8188 (t0) REVERT: A 415 ASP cc_start: 0.8013 (t0) cc_final: 0.7808 (t70) REVERT: A 464 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4947 (tm) REVERT: A 558 ASN cc_start: 0.8088 (m110) cc_final: 0.7240 (m110) REVERT: A 632 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8322 (tm-30) REVERT: A 637 ASP cc_start: 0.8268 (m-30) cc_final: 0.7890 (m-30) REVERT: A 720 MET cc_start: 0.8175 (mtp) cc_final: 0.7878 (mtp) REVERT: A 726 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7655 (mmtp) REVERT: B 209 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8117 (ttm-80) REVERT: B 232 TYR cc_start: 0.8473 (p90) cc_final: 0.7714 (p90) REVERT: F 15 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.7875 (tmm) REVERT: F 156 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8112 (tppp) REVERT: H 1 MET cc_start: 0.8623 (ptp) cc_final: 0.8358 (pmm) REVERT: H 53 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8807 (ttt) REVERT: H 55 TYR cc_start: 0.9097 (t80) cc_final: 0.8882 (t80) REVERT: H 74 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: H 120 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7402 (mm-30) REVERT: G 6 GLU cc_start: 0.8446 (tt0) cc_final: 0.8161 (mt-10) REVERT: I 15 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8149 (tmm) REVERT: I 93 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7707 (mtp85) REVERT: I 151 ASN cc_start: 0.8218 (t0) cc_final: 0.7572 (t0) REVERT: J 21 GLU cc_start: 0.7620 (tp30) cc_final: 0.6819 (tp30) REVERT: J 39 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7641 (mtt) REVERT: J 47 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7575 (pptt) REVERT: J 119 ASP cc_start: 0.8525 (p0) cc_final: 0.8228 (p0) REVERT: J 151 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7124 (mp0) REVERT: J 186 LEU cc_start: 0.8345 (tt) cc_final: 0.7995 (tt) REVERT: J 204 ASP cc_start: 0.7568 (m-30) cc_final: 0.6380 (p0) REVERT: C 44 ASN cc_start: 0.8036 (p0) cc_final: 0.7690 (p0) REVERT: D 97 GLU cc_start: 0.8568 (tt0) cc_final: 0.8169 (tt0) REVERT: E 34 ILE cc_start: 0.8781 (mm) cc_final: 0.8477 (mp) REVERT: E 106 ASP cc_start: 0.7970 (t0) cc_final: 0.7763 (t0) REVERT: E 129 PHE cc_start: 0.8667 (t80) cc_final: 0.8322 (t80) outliers start: 78 outliers final: 41 residues processed: 457 average time/residue: 0.4808 time to fit residues: 259.6838 Evaluate side-chains 441 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 392 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 93 ARG Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 228 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 127 optimal weight: 0.0970 chunk 179 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 178 optimal weight: 0.0670 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129452 restraints weight = 48024.232| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.07 r_work: 0.3504 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22574 Z= 0.129 Angle : 0.743 16.481 30731 Z= 0.355 Chirality : 0.065 1.457 3495 Planarity : 0.003 0.050 3683 Dihedral : 12.203 177.148 3626 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.01 % Allowed : 23.12 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2530 helix: 0.65 (0.16), residues: 1068 sheet: -1.23 (0.26), residues: 387 loop : -2.26 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 183 TYR 0.016 0.001 TYR H 176 PHE 0.015 0.001 PHE E 29 TRP 0.007 0.001 TRP A 334 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (22571) covalent geometry : angle 0.73318 / 0.35 (30725) SS BOND : bond 0.01827 / 0.90 ( 3) SS BOND : angle 8.53617 / 4.09 ( 6) hydrogen bonds : bond 0.03649 / 2.42 ( 961) hydrogen bonds : angle 4.68867 / 3.26 ( 2776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 448 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5049 (ttp) cc_final: 0.4782 (tpp) REVERT: A 173 GLU cc_start: 0.6809 (pp20) cc_final: 0.6549 (tm-30) REVERT: A 253 ASP cc_start: 0.8872 (t0) cc_final: 0.8110 (t0) REVERT: A 415 ASP cc_start: 0.7892 (t0) cc_final: 0.7581 (t70) REVERT: A 420 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7741 (pp) REVERT: A 464 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5085 (tm) REVERT: A 553 PHE cc_start: 0.6580 (m-80) cc_final: 0.6285 (m-80) REVERT: A 558 ASN cc_start: 0.8044 (m110) cc_final: 0.7186 (m110) REVERT: A 632 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 637 ASP cc_start: 0.8232 (m-30) cc_final: 0.7803 (m-30) REVERT: A 720 MET cc_start: 0.8187 (mtp) cc_final: 0.7917 (mtp) REVERT: A 726 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7604 (mmtp) REVERT: B 209 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8092 (ttm-80) REVERT: B 232 TYR cc_start: 0.8392 (p90) cc_final: 0.7817 (p90) REVERT: F 15 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.7870 (tmm) REVERT: F 87 ASP cc_start: 0.8211 (t0) cc_final: 0.7974 (m-30) REVERT: F 120 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: F 156 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8117 (tppp) REVERT: H 173 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8163 (mt-10) REVERT: G 6 GLU cc_start: 0.8407 (tt0) cc_final: 0.8118 (mt-10) REVERT: I 151 ASN cc_start: 0.8196 (t0) cc_final: 0.7629 (t0) REVERT: J 21 GLU cc_start: 0.7624 (tp30) cc_final: 0.6815 (tp30) REVERT: J 39 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: J 47 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7548 (pptt) REVERT: J 119 ASP cc_start: 0.8568 (p0) cc_final: 0.8362 (p0) REVERT: J 151 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7106 (mp0) REVERT: J 204 ASP cc_start: 0.7441 (m-30) cc_final: 0.6519 (p0) REVERT: C 44 ASN cc_start: 0.8082 (p0) cc_final: 0.7752 (p0) REVERT: C 106 ASP cc_start: 0.7927 (t70) cc_final: 0.7291 (t70) REVERT: D 97 GLU cc_start: 0.8584 (tt0) cc_final: 0.8176 (tt0) REVERT: E 70 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8043 (ttt-90) REVERT: E 106 ASP cc_start: 0.8032 (t0) cc_final: 0.7783 (t0) REVERT: E 129 PHE cc_start: 0.8533 (t80) cc_final: 0.8250 (t80) outliers start: 67 outliers final: 32 residues processed: 478 average time/residue: 0.4869 time to fit residues: 276.1135 Evaluate side-chains 439 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 400 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 250 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN D 109 GLN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 65 ASN E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126079 restraints weight = 40110.726| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.81 r_work: 0.3467 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22574 Z= 0.169 Angle : 0.787 16.467 30731 Z= 0.376 Chirality : 0.068 1.508 3495 Planarity : 0.004 0.066 3683 Dihedral : 12.258 179.144 3626 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.28 % Allowed : 24.20 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2530 helix: 0.63 (0.16), residues: 1070 sheet: -1.22 (0.26), residues: 386 loop : -2.22 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 183 TYR 0.019 0.001 TYR F 55 PHE 0.017 0.001 PHE A 73 TRP 0.006 0.001 TRP A 334 HIS 0.004 0.001 HIS G 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (22571) covalent geometry : angle 0.77746 / 0.37 (30725) SS BOND : bond 0.01985 / 0.97 ( 3) SS BOND : angle 8.55889 / 4.10 ( 6) hydrogen bonds : bond 0.03831 / 2.53 ( 961) hydrogen bonds : angle 4.73461 / 3.29 ( 2776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 396 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5006 (ttp) cc_final: 0.4766 (tpp) REVERT: A 86 MET cc_start: 0.4109 (pmm) cc_final: 0.3505 (pmm) REVERT: A 173 GLU cc_start: 0.6754 (pp20) cc_final: 0.6518 (tm-30) REVERT: A 219 ASP cc_start: 0.7688 (m-30) cc_final: 0.7247 (m-30) REVERT: A 253 ASP cc_start: 0.8904 (t0) cc_final: 0.8118 (t0) REVERT: A 293 GLU cc_start: 0.7858 (tt0) cc_final: 0.7575 (tm-30) REVERT: A 358 MET cc_start: 0.7762 (tpp) cc_final: 0.7481 (tpt) REVERT: A 419 GLU cc_start: 0.8523 (pp20) cc_final: 0.8067 (pp20) REVERT: A 464 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.5141 (tm) REVERT: A 558 ASN cc_start: 0.8022 (m110) cc_final: 0.7163 (m110) REVERT: A 632 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 637 ASP cc_start: 0.8106 (m-30) cc_final: 0.7637 (m-30) REVERT: A 665 THR cc_start: 0.8927 (m) cc_final: 0.8719 (t) REVERT: A 693 TYR cc_start: 0.8588 (m-80) cc_final: 0.8372 (m-80) REVERT: A 720 MET cc_start: 0.8181 (mtp) cc_final: 0.7950 (mtp) REVERT: A 726 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7681 (mmtp) REVERT: B 209 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.7851 (ttm-80) REVERT: B 232 TYR cc_start: 0.8386 (p90) cc_final: 0.7826 (p90) REVERT: F 87 ASP cc_start: 0.8202 (t0) cc_final: 0.7968 (m-30) REVERT: F 156 LYS cc_start: 0.8528 (mmtm) cc_final: 0.8217 (tppp) REVERT: H 53 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8777 (ttp) REVERT: H 173 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8164 (mt-10) REVERT: G 6 GLU cc_start: 0.8380 (tt0) cc_final: 0.8088 (mt-10) REVERT: I 22 ASP cc_start: 0.7817 (m-30) cc_final: 0.7592 (m-30) REVERT: J 21 GLU cc_start: 0.7558 (tp30) cc_final: 0.6797 (tp30) REVERT: J 39 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7635 (mtt) REVERT: J 47 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7655 (pptt) REVERT: J 119 ASP cc_start: 0.8562 (p0) cc_final: 0.8341 (p0) REVERT: C 44 ASN cc_start: 0.8056 (p0) cc_final: 0.7738 (p0) REVERT: C 122 ASN cc_start: 0.8839 (m110) cc_final: 0.8481 (m110) REVERT: D 54 THR cc_start: 0.8437 (m) cc_final: 0.8163 (t) REVERT: D 97 GLU cc_start: 0.8554 (tt0) cc_final: 0.8108 (tt0) REVERT: E 70 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: E 81 GLU cc_start: 0.7433 (mp0) cc_final: 0.7227 (mp0) REVERT: E 105 LYS cc_start: 0.7504 (ttmm) cc_final: 0.7041 (ttmm) REVERT: E 106 ASP cc_start: 0.8018 (t0) cc_final: 0.7748 (t0) REVERT: E 109 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8437 (tm-30) REVERT: E 123 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: E 129 PHE cc_start: 0.8581 (t80) cc_final: 0.8259 (t80) outliers start: 73 outliers final: 41 residues processed: 427 average time/residue: 0.4740 time to fit residues: 240.4938 Evaluate side-chains 437 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 390 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 123 GLN Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 95 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 227 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 43 optimal weight: 0.0980 chunk 193 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN D 109 GLN E 18 ASN E 50 GLN E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128045 restraints weight = 50035.322| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.15 r_work: 0.3481 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22574 Z= 0.147 Angle : 0.773 16.342 30731 Z= 0.370 Chirality : 0.066 1.452 3495 Planarity : 0.004 0.061 3683 Dihedral : 12.240 177.617 3626 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 3.10 % Allowed : 24.70 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2530 helix: 0.68 (0.16), residues: 1072 sheet: -1.16 (0.27), residues: 360 loop : -2.19 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 183 TYR 0.018 0.001 TYR F 55 PHE 0.019 0.001 PHE A 73 TRP 0.006 0.001 TRP A 334 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (22571) covalent geometry : angle 0.76402 / 0.37 (30725) SS BOND : bond 0.01935 / 0.95 ( 3) SS BOND : angle 8.60045 / 4.12 ( 6) hydrogen bonds : bond 0.03705 / 2.45 ( 961) hydrogen bonds : angle 4.69837 / 3.27 ( 2776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 411 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5182 (ttp) cc_final: 0.4903 (tpp) REVERT: A 86 MET cc_start: 0.4073 (pmm) cc_final: 0.3516 (pmm) REVERT: A 161 MET cc_start: 0.6512 (tmm) cc_final: 0.5031 (ttt) REVERT: A 173 GLU cc_start: 0.6838 (pp20) cc_final: 0.6608 (tm-30) REVERT: A 219 ASP cc_start: 0.7729 (m-30) cc_final: 0.7268 (m-30) REVERT: A 253 ASP cc_start: 0.8922 (t0) cc_final: 0.8086 (t0) REVERT: A 358 MET cc_start: 0.7817 (tpp) cc_final: 0.7587 (tpt) REVERT: A 419 GLU cc_start: 0.8530 (pp20) cc_final: 0.8281 (pp20) REVERT: A 464 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.5126 (tm) REVERT: A 558 ASN cc_start: 0.8082 (m110) cc_final: 0.7248 (m110) REVERT: A 632 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 637 ASP cc_start: 0.8125 (m-30) cc_final: 0.7684 (m-30) REVERT: A 665 THR cc_start: 0.8913 (m) cc_final: 0.8705 (t) REVERT: A 720 MET cc_start: 0.8162 (mtp) cc_final: 0.7904 (mtp) REVERT: A 726 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7611 (mmtt) REVERT: B 21 GLU cc_start: 0.7514 (pp20) cc_final: 0.7030 (pt0) REVERT: B 209 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.7797 (ttm-80) REVERT: B 232 TYR cc_start: 0.8453 (p90) cc_final: 0.7851 (p90) REVERT: F 87 ASP cc_start: 0.8239 (t0) cc_final: 0.7922 (m-30) REVERT: F 156 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8180 (tppp) REVERT: H 55 TYR cc_start: 0.9081 (t80) cc_final: 0.8850 (t80) REVERT: H 173 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8197 (mt-10) REVERT: G 6 GLU cc_start: 0.8359 (tt0) cc_final: 0.8044 (mt-10) REVERT: J 21 GLU cc_start: 0.7592 (tp30) cc_final: 0.6785 (tp30) REVERT: J 39 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7604 (mtt) REVERT: J 47 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7667 (pptt) REVERT: J 119 ASP cc_start: 0.8557 (p0) cc_final: 0.8343 (p0) REVERT: J 151 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7079 (mp0) REVERT: J 157 GLN cc_start: 0.7846 (tt0) cc_final: 0.7518 (mm-40) REVERT: J 160 ASP cc_start: 0.8159 (m-30) cc_final: 0.7799 (m-30) REVERT: J 204 ASP cc_start: 0.7515 (m-30) cc_final: 0.7184 (p0) REVERT: C 44 ASN cc_start: 0.8114 (p0) cc_final: 0.7810 (p0) REVERT: C 106 ASP cc_start: 0.7923 (t70) cc_final: 0.7275 (t70) REVERT: C 122 ASN cc_start: 0.8926 (m110) cc_final: 0.8589 (m110) REVERT: D 19 GLU cc_start: 0.7258 (pm20) cc_final: 0.7029 (pm20) REVERT: D 54 THR cc_start: 0.8468 (m) cc_final: 0.8140 (t) REVERT: E 70 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7963 (ttt-90) REVERT: E 81 GLU cc_start: 0.7476 (mp0) cc_final: 0.7246 (mp0) REVERT: E 82 ASN cc_start: 0.8171 (m110) cc_final: 0.7639 (p0) REVERT: E 105 LYS cc_start: 0.7434 (ttmm) cc_final: 0.6786 (ttmm) REVERT: E 106 ASP cc_start: 0.7959 (t0) cc_final: 0.7662 (t0) REVERT: E 129 PHE cc_start: 0.8506 (t80) cc_final: 0.8155 (t80) outliers start: 69 outliers final: 41 residues processed: 444 average time/residue: 0.4770 time to fit residues: 251.8420 Evaluate side-chains 437 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 392 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 62 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 16 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN J 214 GLN J 215 ASN D 109 GLN E 18 ASN E 50 GLN E 69 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124361 restraints weight = 42708.916| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.97 r_work: 0.3430 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22574 Z= 0.202 Angle : 0.827 16.602 30731 Z= 0.397 Chirality : 0.070 1.495 3495 Planarity : 0.004 0.057 3683 Dihedral : 12.314 178.071 3626 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.40 % Favored : 93.56 % Rotamer: Outliers : 3.10 % Allowed : 25.24 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.16), residues: 2530 helix: 0.55 (0.16), residues: 1073 sheet: -1.25 (0.26), residues: 367 loop : -2.21 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 183 TYR 0.021 0.002 TYR F 55 PHE 0.022 0.001 PHE A 73 TRP 0.005 0.001 TRP A 186 HIS 0.005 0.001 HIS G 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (22571) covalent geometry : angle 0.81804 / 0.39 (30725) SS BOND : bond 0.01996 / 0.98 ( 3) SS BOND : angle 8.70057 / 4.18 ( 6) hydrogen bonds : bond 0.04029 / 2.65 ( 961) hydrogen bonds : angle 4.83088 / 3.36 ( 2776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 396 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4889 (ttp) cc_final: 0.4675 (tpp) REVERT: A 86 MET cc_start: 0.4223 (pmm) cc_final: 0.3683 (pmm) REVERT: A 219 ASP cc_start: 0.7857 (m-30) cc_final: 0.7375 (m-30) REVERT: A 253 ASP cc_start: 0.8958 (t0) cc_final: 0.8162 (t0) REVERT: A 358 MET cc_start: 0.7845 (tpp) cc_final: 0.7538 (tpt) REVERT: A 420 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7843 (pp) REVERT: A 464 LEU cc_start: 0.5692 (OUTLIER) cc_final: 0.5320 (tm) REVERT: A 558 ASN cc_start: 0.8126 (m110) cc_final: 0.7309 (m110) REVERT: A 632 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 637 ASP cc_start: 0.8214 (m-30) cc_final: 0.7780 (m-30) REVERT: A 665 THR cc_start: 0.8908 (m) cc_final: 0.8672 (t) REVERT: A 693 TYR cc_start: 0.8585 (m-80) cc_final: 0.8333 (m-80) REVERT: A 720 MET cc_start: 0.8170 (mtp) cc_final: 0.7860 (mtp) REVERT: A 726 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7638 (mmtp) REVERT: B 21 GLU cc_start: 0.7608 (pp20) cc_final: 0.7063 (pt0) REVERT: B 209 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: B 232 TYR cc_start: 0.8437 (p90) cc_final: 0.8014 (p90) REVERT: F 156 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8136 (tppp) REVERT: G 125 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8669 (mtt180) REVERT: J 21 GLU cc_start: 0.7563 (tp30) cc_final: 0.6742 (tp30) REVERT: J 39 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7662 (mtt) REVERT: J 47 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7628 (pptt) REVERT: J 119 ASP cc_start: 0.8486 (p0) cc_final: 0.8187 (p0) REVERT: J 157 GLN cc_start: 0.7921 (tt0) cc_final: 0.7559 (mm-40) REVERT: J 160 ASP cc_start: 0.8196 (m-30) cc_final: 0.7866 (m-30) REVERT: J 214 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: C 20 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8107 (mtmm) REVERT: C 44 ASN cc_start: 0.8102 (p0) cc_final: 0.7814 (p0) REVERT: C 118 THR cc_start: 0.8856 (p) cc_final: 0.8451 (p) REVERT: C 122 ASN cc_start: 0.8941 (m110) cc_final: 0.8614 (m110) REVERT: E 70 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8139 (ttt-90) REVERT: E 81 GLU cc_start: 0.7424 (mp0) cc_final: 0.7167 (mp0) REVERT: E 82 ASN cc_start: 0.8211 (m110) cc_final: 0.7845 (OUTLIER) REVERT: E 105 LYS cc_start: 0.7633 (ttmm) cc_final: 0.7323 (ttmm) REVERT: E 106 ASP cc_start: 0.7983 (t0) cc_final: 0.7648 (t0) outliers start: 69 outliers final: 41 residues processed: 431 average time/residue: 0.4678 time to fit residues: 240.4217 Evaluate side-chains 422 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 375 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 214 GLN Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 76 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 221 optimal weight: 0.4980 chunk 142 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN J 38 HIS J 215 ASN E 50 GLN E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122816 restraints weight = 50776.565| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.43 r_work: 0.3401 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 22574 Z= 0.225 Angle : 0.859 18.497 30731 Z= 0.414 Chirality : 0.071 1.526 3495 Planarity : 0.004 0.055 3683 Dihedral : 12.388 178.621 3626 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 2.38 % Allowed : 26.14 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.16), residues: 2530 helix: 0.46 (0.16), residues: 1078 sheet: -1.32 (0.26), residues: 372 loop : -2.28 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 183 TYR 0.023 0.002 TYR F 55 PHE 0.025 0.002 PHE A 73 TRP 0.005 0.001 TRP A 186 HIS 0.005 0.001 HIS G 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (22571) covalent geometry : angle 0.85037 / 0.41 (30725) SS BOND : bond 0.02461 / 1.20 ( 3) SS BOND : angle 8.62572 / 4.15 ( 6) hydrogen bonds : bond 0.04120 / 2.70 ( 961) hydrogen bonds : angle 4.92132 / 3.43 ( 2776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4933 (ttp) cc_final: 0.4620 (tpp) REVERT: A 86 MET cc_start: 0.4277 (pmm) cc_final: 0.3744 (pmm) REVERT: A 181 MET cc_start: 0.2937 (mmt) cc_final: 0.2295 (mpp) REVERT: A 253 ASP cc_start: 0.8995 (t0) cc_final: 0.8207 (t0) REVERT: A 358 MET cc_start: 0.7891 (tpp) cc_final: 0.7591 (tpt) REVERT: A 419 GLU cc_start: 0.8383 (pp20) cc_final: 0.8087 (pp20) REVERT: A 464 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5279 (tm) REVERT: A 558 ASN cc_start: 0.8178 (m110) cc_final: 0.7340 (m110) REVERT: A 632 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8252 (tm-30) REVERT: A 637 ASP cc_start: 0.8248 (m-30) cc_final: 0.7802 (m-30) REVERT: A 665 THR cc_start: 0.8922 (m) cc_final: 0.8666 (t) REVERT: A 720 MET cc_start: 0.8204 (mtp) cc_final: 0.7989 (mtp) REVERT: A 726 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7664 (mmtp) REVERT: B 21 GLU cc_start: 0.7678 (pp20) cc_final: 0.7104 (pt0) REVERT: B 209 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.7859 (ttm-80) REVERT: B 232 TYR cc_start: 0.8478 (p90) cc_final: 0.8189 (p90) REVERT: F 156 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8211 (tppp) REVERT: H 53 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8831 (ttt) REVERT: H 120 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7365 (mt-10) REVERT: G 125 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8692 (mtt180) REVERT: J 21 GLU cc_start: 0.7562 (tp30) cc_final: 0.6727 (tp30) REVERT: J 39 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7655 (mtt) REVERT: J 47 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7611 (pptt) REVERT: J 119 ASP cc_start: 0.8475 (p0) cc_final: 0.8166 (p0) REVERT: J 151 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7189 (mp0) REVERT: J 157 GLN cc_start: 0.7898 (tt0) cc_final: 0.7566 (mm-40) REVERT: J 160 ASP cc_start: 0.8209 (m-30) cc_final: 0.7871 (m-30) REVERT: J 204 ASP cc_start: 0.7702 (m-30) cc_final: 0.7332 (p0) REVERT: J 214 GLN cc_start: 0.8182 (mt0) cc_final: 0.7637 (mp10) REVERT: J 315 ASP cc_start: 0.7575 (t0) cc_final: 0.7245 (t0) REVERT: C 20 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8178 (mtmm) REVERT: C 44 ASN cc_start: 0.8140 (p0) cc_final: 0.7861 (p0) REVERT: C 118 THR cc_start: 0.8853 (p) cc_final: 0.8455 (p) REVERT: C 122 ASN cc_start: 0.8956 (m110) cc_final: 0.8629 (m110) REVERT: E 70 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8205 (ttt-90) REVERT: E 81 GLU cc_start: 0.7426 (mp0) cc_final: 0.7168 (mp0) REVERT: E 82 ASN cc_start: 0.8194 (m110) cc_final: 0.7856 (OUTLIER) REVERT: E 105 LYS cc_start: 0.7637 (ttmm) cc_final: 0.7311 (ttmm) REVERT: E 106 ASP cc_start: 0.7975 (t0) cc_final: 0.7660 (t0) outliers start: 53 outliers final: 43 residues processed: 408 average time/residue: 0.4583 time to fit residues: 221.7723 Evaluate side-chains 418 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 58 PHE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 307 TYR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 140 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 62 ASN ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN J 214 GLN E 18 ASN E 50 GLN E 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125589 restraints weight = 42422.035| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.02 r_work: 0.3446 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22574 Z= 0.177 Angle : 0.820 18.246 30731 Z= 0.395 Chirality : 0.069 1.504 3495 Planarity : 0.004 0.057 3683 Dihedral : 12.369 178.276 3626 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.32 % Favored : 93.64 % Rotamer: Outliers : 2.52 % Allowed : 26.41 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.16), residues: 2530 helix: 0.51 (0.16), residues: 1079 sheet: -1.20 (0.26), residues: 366 loop : -2.23 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 719 TYR 0.021 0.001 TYR F 55 PHE 0.023 0.001 PHE A 73 TRP 0.006 0.001 TRP A 334 HIS 0.014 0.001 HIS J 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (22571) covalent geometry : angle 0.81159 / 0.39 (30725) SS BOND : bond 0.02188 / 1.07 ( 3) SS BOND : angle 8.55065 / 4.06 ( 6) hydrogen bonds : bond 0.03937 / 2.59 ( 961) hydrogen bonds : angle 4.85861 / 3.39 ( 2776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8294.74 seconds wall clock time: 142 minutes 19.38 seconds (8539.38 seconds total)