Starting phenix.real_space_refine on Sun Aug 9 23:56:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nlv_49523/08_2026/9nlv_49523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nlv_49523/08_2026/9nlv_49523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nlv_49523/08_2026/9nlv_49523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nlv_49523/08_2026/9nlv_49523.map" model { file = "/net/cci-nas-00/data/ceres_data/9nlv_49523/08_2026/9nlv_49523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nlv_49523/08_2026/9nlv_49523.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 846 5.49 5 S 48 5.16 5 C 22860 2.51 5 N 7146 2.21 5 O 9780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40680 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "B" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "C" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "D" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "E" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "F" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "K" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "L" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Time building chain proxies: 7.03, per 1000 atoms: 0.17 Number of scatterers: 40680 At special positions: 0 Unit cell: (196.624, 177.596, 142.258, 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 48 16.00 P 846 15.00 O 9780 8.00 N 7146 7.00 C 22860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 18 sheets defined 59.8% alpha, 5.9% beta 84 base pairs and 420 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER A 56 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.792A pdb=" N ILE A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.537A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 336 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS A 341 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'B' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER B 56 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.538A pdb=" N ALA B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.563A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 262 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.775A pdb=" N LYS B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 370 removed outlier: 3.530A pdb=" N LEU B 359 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 403 through 432 removed outlier: 3.601A pdb=" N LEU B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 468 through 484 removed outlier: 3.780A pdb=" N ILE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 482 " --> pdb=" O LYS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'C' and resid 2 through 41 removed outlier: 3.666A pdb=" N GLN C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER C 56 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 69 through 83 removed outlier: 3.792A pdb=" N ILE C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.538A pdb=" N ALA C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 272 removed outlier: 3.740A pdb=" N PHE C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 336 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS C 341 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 482 " --> pdb=" O LYS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'D' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN D 6 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 27 " --> pdb=" O HIS D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER D 56 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.538A pdb=" N ALA D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.758A pdb=" N LEU D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 272 removed outlier: 3.742A pdb=" N PHE D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 262 " --> pdb=" O CYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 336 Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS D 341 " --> pdb=" O PRO D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU D 359 " --> pdb=" O ASP D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'D' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'D' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 482 " --> pdb=" O LYS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'E' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN E 6 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN E 27 " --> pdb=" O HIS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 44 No H-bonds generated for 'chain 'E' and resid 42 through 44' Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER E 56 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 124 " --> pdb=" O PHE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 144 through 159 removed outlier: 3.537A pdb=" N ALA E 148 " --> pdb=" O ASN E 144 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS E 158 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN E 262 " --> pdb=" O CYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 336 Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS E 341 " --> pdb=" O PRO E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU E 359 " --> pdb=" O ASP E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 383 Processing helix chain 'E' and resid 393 through 398 Processing helix chain 'E' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 447 No H-bonds generated for 'chain 'E' and resid 445 through 447' Processing helix chain 'E' and resid 448 through 454 Processing helix chain 'E' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN E 481 " --> pdb=" O GLN E 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 482 " --> pdb=" O LYS E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 489 Processing helix chain 'F' and resid 2 through 41 removed outlier: 3.666A pdb=" N GLN F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN F 27 " --> pdb=" O HIS F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 44 No H-bonds generated for 'chain 'F' and resid 42 through 44' Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER F 56 " --> pdb=" O ASN F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 61 Processing helix chain 'F' and resid 62 through 69 Processing helix chain 'F' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE F 73 " --> pdb=" O ASN F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 124 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.537A pdb=" N ALA F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 193 through 203 removed outlier: 3.563A pdb=" N PHE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE F 261 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN F 262 " --> pdb=" O CYS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 336 Processing helix chain 'F' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS F 341 " --> pdb=" O PRO F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU F 359 " --> pdb=" O ASP F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 383 Processing helix chain 'F' and resid 393 through 398 Processing helix chain 'F' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 447 No H-bonds generated for 'chain 'F' and resid 445 through 447' Processing helix chain 'F' and resid 448 through 454 Processing helix chain 'F' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN F 481 " --> pdb=" O GLN F 477 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 482 " --> pdb=" O LYS F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR A 247 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 167 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS A 298 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 285 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS A 274 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR B 247 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE B 167 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS B 298 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 285 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 4.719A pdb=" N LYS B 274 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA7, first strand: chain 'C' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR C 247 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE C 167 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS C 298 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 285 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS C 274 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'D' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR D 247 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE D 167 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LYS D 298 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 285 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS D 274 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 301 through 303 Processing sheet with id=AB4, first strand: chain 'E' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR E 247 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE E 167 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS E 298 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU E 285 " --> pdb=" O LYS E 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.719A pdb=" N LYS E 274 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 301 through 303 Processing sheet with id=AB7, first strand: chain 'F' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR F 247 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE F 167 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS F 298 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU F 285 " --> pdb=" O LYS F 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS F 274 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 303 1212 hydrogen bonds defined for protein. 3438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 186 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 420 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7114 1.33 - 1.45: 14771 1.45 - 1.57: 19683 1.57 - 1.69: 1686 1.69 - 1.81: 66 Bond restraints: 43320 Sorted by residual: bond pdb=" CA ILE A 103 " pdb=" C ILE A 103 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.27e-02 6.20e+03 4.35e+00 bond pdb=" CA ILE E 103 " pdb=" C ILE E 103 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.27e-02 6.20e+03 4.16e+00 bond pdb=" CA ILE C 103 " pdb=" C ILE C 103 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 4.02e+00 bond pdb=" CA ILE F 103 " pdb=" C ILE F 103 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 4.02e+00 bond pdb=" CA ILE B 103 " pdb=" C ILE B 103 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.27e-02 6.20e+03 3.92e+00 ... (remaining 43315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 57545 1.39 - 2.78: 4421 2.78 - 4.18: 649 4.18 - 5.57: 115 5.57 - 6.96: 30 Bond angle restraints: 62760 Sorted by residual: angle pdb=" N ILE D 103 " pdb=" CA ILE D 103 " pdb=" C ILE D 103 " ideal model delta sigma weight residual 110.62 103.66 6.96 1.02e+00 9.61e-01 4.66e+01 angle pdb=" N ILE C 103 " pdb=" CA ILE C 103 " pdb=" C ILE C 103 " ideal model delta sigma weight residual 110.62 103.68 6.94 1.02e+00 9.61e-01 4.62e+01 angle pdb=" N ILE A 103 " pdb=" CA ILE A 103 " pdb=" C ILE A 103 " ideal model delta sigma weight residual 110.62 103.69 6.93 1.02e+00 9.61e-01 4.62e+01 angle pdb=" N ILE E 103 " pdb=" CA ILE E 103 " pdb=" C ILE E 103 " ideal model delta sigma weight residual 110.62 103.69 6.93 1.02e+00 9.61e-01 4.62e+01 angle pdb=" N ILE B 103 " pdb=" CA ILE B 103 " pdb=" C ILE B 103 " ideal model delta sigma weight residual 110.62 103.70 6.92 1.02e+00 9.61e-01 4.61e+01 ... (remaining 62755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 23876 35.31 - 70.63: 2776 70.63 - 105.94: 348 105.94 - 141.25: 30 141.25 - 176.57: 48 Dihedral angle restraints: 27078 sinusoidal: 18360 harmonic: 8718 Sorted by residual: dihedral pdb=" O4' U J 138 " pdb=" C1' U J 138 " pdb=" N1 U J 138 " pdb=" C2 U J 138 " ideal model delta sinusoidal sigma weight residual -160.00 -3.72 -156.28 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U I 138 " pdb=" C1' U I 138 " pdb=" N1 U I 138 " pdb=" C2 U I 138 " ideal model delta sinusoidal sigma weight residual -160.00 -3.72 -156.28 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U L 138 " pdb=" C1' U L 138 " pdb=" N1 U L 138 " pdb=" C2 U L 138 " ideal model delta sinusoidal sigma weight residual -160.00 -3.73 -156.27 1 1.50e+01 4.44e-03 8.17e+01 ... (remaining 27075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5844 0.063 - 0.125: 1242 0.125 - 0.188: 561 0.188 - 0.251: 75 0.251 - 0.314: 12 Chirality restraints: 7734 Sorted by residual: chirality pdb=" C3' U H 59 " pdb=" C4' U H 59 " pdb=" O3' U H 59 " pdb=" C2' U H 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C3' U K 59 " pdb=" C4' U K 59 " pdb=" O3' U K 59 " pdb=" C2' U K 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C3' U L 59 " pdb=" C4' U L 59 " pdb=" O3' U L 59 " pdb=" C2' U L 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 7731 not shown) Planarity restraints: 4842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U K 24 " -0.037 2.00e-02 2.50e+03 2.66e-02 1.59e+01 pdb=" N1 U K 24 " 0.067 2.00e-02 2.50e+03 pdb=" C2 U K 24 " -0.021 2.00e-02 2.50e+03 pdb=" O2 U K 24 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U K 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U K 24 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U K 24 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U K 24 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U K 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 24 " -0.037 2.00e-02 2.50e+03 2.66e-02 1.59e+01 pdb=" N1 U I 24 " 0.066 2.00e-02 2.50e+03 pdb=" C2 U I 24 " -0.021 2.00e-02 2.50e+03 pdb=" O2 U I 24 " 0.008 2.00e-02 2.50e+03 pdb=" N3 U I 24 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U I 24 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U I 24 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U I 24 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U I 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 24 " 0.037 2.00e-02 2.50e+03 2.65e-02 1.58e+01 pdb=" N1 U G 24 " -0.066 2.00e-02 2.50e+03 pdb=" C2 U G 24 " 0.021 2.00e-02 2.50e+03 pdb=" O2 U G 24 " -0.008 2.00e-02 2.50e+03 pdb=" N3 U G 24 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U G 24 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U G 24 " 0.004 2.00e-02 2.50e+03 pdb=" C5 U G 24 " 0.006 2.00e-02 2.50e+03 pdb=" C6 U G 24 " 0.001 2.00e-02 2.50e+03 ... (remaining 4839 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 11842 2.81 - 3.33: 34629 3.33 - 3.86: 75409 3.86 - 4.38: 84814 4.38 - 4.90: 123668 Nonbonded interactions: 330362 Sorted by model distance: nonbonded pdb=" O4' U G 138 " pdb=" O2 U G 138 " model vdw 2.290 3.040 nonbonded pdb=" O4' U H 138 " pdb=" O2 U H 138 " model vdw 2.291 3.040 nonbonded pdb=" O4' U L 138 " pdb=" O2 U L 138 " model vdw 2.291 3.040 nonbonded pdb=" O4' U I 138 " pdb=" O2 U I 138 " model vdw 2.291 3.040 nonbonded pdb=" O4' U J 138 " pdb=" O2 U J 138 " model vdw 2.292 3.040 ... (remaining 330357 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.830 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.880 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 : 0.004 0.036 43320 Z= 0.285 Angle : 0.814 6.960 62760 Z= 0.643 Chirality : 0.063 0.314 7734 Planarity : 0.005 0.040 4842 Dihedral : 25.686 176.567 21438 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 21.02 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % 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: -0.76 (0.14), residues: 2940 helix: -0.16 (0.12), residues: 1410 sheet: 0.13 (0.40), residues: 132 loop : -0.82 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 9 TYR 0.015 0.001 TYR C 70 PHE 0.012 0.001 PHE F 120 TRP 0.010 0.001 TRP D 432 HIS 0.006 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.29 (43320) covalent geometry : angle 0.81380 / 0.64 (62760) hydrogen bonds : bond 0.21600 / 14.39 ( 1398) hydrogen bonds : angle 6.68930 / 4.83 ( 3642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.905 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.8100 time to fit residues: 45.1501 Evaluate side-chains 45 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.089798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.054492 restraints weight = 105840.268| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.06 r_work: 0.2740 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43320 Z= 0.154 Angle : 0.586 11.121 62760 Z= 0.338 Chirality : 0.045 0.598 7734 Planarity : 0.004 0.038 4842 Dihedral : 26.201 178.273 16452 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.57 % Allowed : 17.42 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % 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: 0.94 (0.15), residues: 2940 helix: 1.81 (0.13), residues: 1494 sheet: 0.24 (0.36), residues: 132 loop : -0.74 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 9 TYR 0.014 0.001 TYR D 70 PHE 0.011 0.001 PHE F 120 TRP 0.012 0.002 TRP E 250 HIS 0.009 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (43320) covalent geometry : angle 0.58623 / 0.34 (62760) hydrogen bonds : bond 0.09687 / 6.55 ( 1398) hydrogen bonds : angle 4.20966 / 3.01 ( 3642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.732 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 0.5715 time to fit residues: 39.7847 Evaluate side-chains 39 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 133 optimal weight: 0.8980 chunk 355 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 0.0050 chunk 141 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 273 optimal weight: 0.6980 chunk 146 optimal weight: 0.2980 chunk 59 optimal weight: 10.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056667 restraints weight = 107461.765| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.08 r_work: 0.2797 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 43320 Z= 0.122 Angle : 0.491 10.847 62760 Z= 0.287 Chirality : 0.040 0.392 7734 Planarity : 0.004 0.069 4842 Dihedral : 25.676 179.212 16452 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.33 % Allowed : 17.28 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % 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: 1.51 (0.15), residues: 2940 helix: 2.36 (0.13), residues: 1500 sheet: 0.32 (0.35), residues: 132 loop : -0.57 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 9 TYR 0.013 0.001 TYR A 329 PHE 0.009 0.001 PHE A 167 TRP 0.010 0.001 TRP E 250 HIS 0.005 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (43320) covalent geometry : angle 0.49095 / 0.29 (62760) hydrogen bonds : bond 0.08071 / 5.45 ( 1398) hydrogen bonds : angle 3.73737 / 2.68 ( 3642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 1.082 Fit side-chains outliers start: 28 outliers final: 6 residues processed: 68 average time/residue: 0.5370 time to fit residues: 48.0443 Evaluate side-chains 44 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 356 optimal weight: 50.0000 chunk 4 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 290 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.087882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.051594 restraints weight = 104501.781| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.06 r_work: 0.2657 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43320 Z= 0.197 Angle : 0.580 11.442 62760 Z= 0.326 Chirality : 0.045 0.507 7734 Planarity : 0.004 0.082 4842 Dihedral : 25.500 179.913 16452 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.66 % Allowed : 17.05 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % 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: 1.59 (0.16), residues: 2940 helix: 2.50 (0.13), residues: 1506 sheet: 0.27 (0.34), residues: 132 loop : -0.63 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 9 TYR 0.016 0.002 TYR D 329 PHE 0.022 0.002 PHE F 120 TRP 0.014 0.002 TRP E 250 HIS 0.012 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (43320) covalent geometry : angle 0.57959 / 0.33 (62760) hydrogen bonds : bond 0.10477 / 7.06 ( 1398) hydrogen bonds : angle 3.92504 / 2.82 ( 3642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 1.024 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 44 average time/residue: 0.4028 time to fit residues: 25.4170 Evaluate side-chains 44 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 221 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 306 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 377 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.054863 restraints weight = 105608.391| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.05 r_work: 0.2746 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 43320 Z= 0.108 Angle : 0.476 10.947 62760 Z= 0.277 Chirality : 0.039 0.434 7734 Planarity : 0.003 0.022 4842 Dihedral : 25.314 178.751 16452 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.99 % Allowed : 16.62 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % 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: 1.95 (0.16), residues: 2940 helix: 2.87 (0.13), residues: 1506 sheet: 0.38 (0.35), residues: 132 loop : -0.55 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 9 TYR 0.011 0.001 TYR D 70 PHE 0.008 0.001 PHE D 440 TRP 0.011 0.001 TRP E 250 HIS 0.004 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.11 (43320) covalent geometry : angle 0.47647 / 0.28 (62760) hydrogen bonds : bond 0.07817 / 5.27 ( 1398) hydrogen bonds : angle 3.52650 / 2.53 ( 3642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.848 Fit side-chains outliers start: 21 outliers final: 4 residues processed: 55 average time/residue: 0.4735 time to fit residues: 34.8166 Evaluate side-chains 38 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 319 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.051936 restraints weight = 104753.389| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.04 r_work: 0.2666 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43320 Z= 0.174 Angle : 0.538 11.019 62760 Z= 0.302 Chirality : 0.043 0.472 7734 Planarity : 0.004 0.036 4842 Dihedral : 25.207 179.310 16452 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.85 % Allowed : 15.96 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % 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: 1.87 (0.16), residues: 2940 helix: 2.82 (0.13), residues: 1506 sheet: 0.34 (0.35), residues: 132 loop : -0.62 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 9 TYR 0.015 0.001 TYR E 306 PHE 0.017 0.001 PHE F 120 TRP 0.013 0.002 TRP E 250 HIS 0.010 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (43320) covalent geometry : angle 0.53758 / 0.30 (62760) hydrogen bonds : bond 0.09670 / 6.51 ( 1398) hydrogen bonds : angle 3.75708 / 2.70 ( 3642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.814 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 48 average time/residue: 0.3988 time to fit residues: 27.4669 Evaluate side-chains 44 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 359 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 266 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 85 optimal weight: 0.0170 chunk 353 optimal weight: 40.0000 chunk 184 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 231 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.091240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.055531 restraints weight = 105260.221| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.03 r_work: 0.2762 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 43320 Z= 0.109 Angle : 0.470 10.574 62760 Z= 0.270 Chirality : 0.039 0.422 7734 Planarity : 0.003 0.022 4842 Dihedral : 25.020 178.923 16452 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.76 % Allowed : 16.24 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.16), residues: 2940 helix: 2.94 (0.13), residues: 1506 sheet: 0.50 (0.36), residues: 132 loop : -0.50 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.010 0.001 TYR C 329 PHE 0.007 0.001 PHE D 440 TRP 0.010 0.001 TRP C 250 HIS 0.003 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.11 (43320) covalent geometry : angle 0.46981 / 0.27 (62760) hydrogen bonds : bond 0.07414 / 4.97 ( 1398) hydrogen bonds : angle 3.41090 / 2.45 ( 3642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.812 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 50 average time/residue: 0.4489 time to fit residues: 31.1737 Evaluate side-chains 43 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 235 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 173 optimal weight: 0.8980 chunk 300 optimal weight: 0.9990 chunk 334 optimal weight: 40.0000 chunk 287 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.089665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.053461 restraints weight = 104232.196| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.03 r_work: 0.2706 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43320 Z= 0.142 Angle : 0.493 10.305 62760 Z= 0.278 Chirality : 0.040 0.438 7734 Planarity : 0.003 0.028 4842 Dihedral : 24.933 178.730 16452 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.66 % Allowed : 16.15 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.16), residues: 2940 helix: 3.00 (0.13), residues: 1506 sheet: 0.47 (0.36), residues: 132 loop : -0.53 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 366 TYR 0.013 0.001 TYR D 329 PHE 0.012 0.001 PHE C 120 TRP 0.013 0.001 TRP E 250 HIS 0.008 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (43320) covalent geometry : angle 0.49281 / 0.28 (62760) hydrogen bonds : bond 0.08474 / 5.68 ( 1398) hydrogen bonds : angle 3.53163 / 2.54 ( 3642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 49 average time/residue: 0.5740 time to fit residues: 36.8339 Evaluate side-chains 42 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 230 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 367 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 222 optimal weight: 2.9990 chunk 241 optimal weight: 0.0970 chunk 54 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.089871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053675 restraints weight = 104893.259| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.03 r_work: 0.2712 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 43320 Z= 0.124 Angle : 0.483 10.117 62760 Z= 0.273 Chirality : 0.040 0.446 7734 Planarity : 0.003 0.024 4842 Dihedral : 24.901 179.023 16452 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.71 % Allowed : 15.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.16), residues: 2940 helix: 3.05 (0.13), residues: 1506 sheet: 0.51 (0.36), residues: 132 loop : -0.56 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 9 TYR 0.012 0.001 TYR D 70 PHE 0.011 0.001 PHE F 120 TRP 0.012 0.001 TRP E 250 HIS 0.007 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (43320) covalent geometry : angle 0.48346 / 0.27 (62760) hydrogen bonds : bond 0.08243 / 5.53 ( 1398) hydrogen bonds : angle 3.50520 / 2.52 ( 3642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 49 average time/residue: 0.6640 time to fit residues: 41.5509 Evaluate side-chains 40 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 356 optimal weight: 40.0000 chunk 315 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 0.5980 chunk 354 optimal weight: 50.0000 chunk 45 optimal weight: 0.0770 chunk 111 optimal weight: 0.9980 chunk 364 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.090426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054358 restraints weight = 104020.780| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.02 r_work: 0.2730 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43320 Z= 0.108 Angle : 0.469 9.904 62760 Z= 0.267 Chirality : 0.039 0.435 7734 Planarity : 0.003 0.024 4842 Dihedral : 24.881 178.678 16452 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.33 % Allowed : 16.34 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.16), residues: 2940 helix: 3.09 (0.13), residues: 1506 sheet: 0.59 (0.37), residues: 132 loop : -0.50 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 9 TYR 0.012 0.001 TYR D 329 PHE 0.008 0.001 PHE D 440 TRP 0.014 0.001 TRP B 250 HIS 0.006 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.11 (43320) covalent geometry : angle 0.46871 / 0.27 (62760) hydrogen bonds : bond 0.07910 / 5.30 ( 1398) hydrogen bonds : angle 3.45545 / 2.48 ( 3642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.5952 time to fit residues: 30.9690 Evaluate side-chains 39 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 248 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 217 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 184 optimal weight: 0.0370 overall best weight: 2.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.088515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052030 restraints weight = 104243.260| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.01 r_work: 0.2665 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43320 Z= 0.182 Angle : 0.531 9.775 62760 Z= 0.296 Chirality : 0.042 0.457 7734 Planarity : 0.004 0.043 4842 Dihedral : 24.830 179.558 16452 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.43 % Allowed : 16.10 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % 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: 1.95 (0.16), residues: 2940 helix: 2.90 (0.13), residues: 1506 sheet: 0.43 (0.35), residues: 132 loop : -0.61 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 207 TYR 0.015 0.001 TYR B 306 PHE 0.015 0.001 PHE F 120 TRP 0.012 0.002 TRP B 250 HIS 0.011 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (43320) covalent geometry : angle 0.53090 / 0.30 (62760) hydrogen bonds : bond 0.09505 / 6.37 ( 1398) hydrogen bonds : angle 3.69246 / 2.65 ( 3642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9618.96 seconds wall clock time: 164 minutes 47.18 seconds (9887.18 seconds total)