Starting phenix.real_space_refine on Thu Nov 20 22:36:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nlv_49523/11_2025/9nlv_49523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nlv_49523/11_2025/9nlv_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nlv_49523/11_2025/9nlv_49523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nlv_49523/11_2025/9nlv_49523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nlv_49523/11_2025/9nlv_49523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nlv_49523/11_2025/9nlv_49523.map" } 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-2.0-5881/lib/python3.9/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: 8.39, per 1000 atoms: 0.21 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: 3.10 Conformation dependent library (CDL) restraints added in 1.2 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: 5.45 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: 8.43 Time building geometry restraints manager: 4.24 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: 59121 1.39 - 2.78: 2998 2.78 - 4.18: 496 4.18 - 5.57: 116 5.57 - 6.96: 29 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: 6433 0.063 - 0.125: 917 0.125 - 0.188: 315 0.188 - 0.251: 57 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: 0.09 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: 11.760 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: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 37.580 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.140 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:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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= 0.219 Angle : 0.713 6.960 62760 Z= 0.454 Chirality : 0.054 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 covalent geometry : bond 0.00379 (43320) covalent geometry : angle 0.71257 (62760) hydrogen bonds : bond 0.21600 ( 1398) hydrogen bonds : angle 6.68930 ( 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 : 1.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 1.0801 time to fit residues: 59.0103 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 : 1.233 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.089692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054170 restraints weight = 105734.573| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.05 r_work: 0.2730 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43320 Z= 0.157 Angle : 0.617 10.781 62760 Z= 0.320 Chirality : 0.039 0.312 7734 Planarity : 0.004 0.029 4842 Dihedral : 25.868 174.641 16452 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.66 % Allowed : 17.23 % Favored : 82.10 % 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: 1.00 (0.15), residues: 2940 helix: 1.92 (0.13), residues: 1500 sheet: -0.04 (0.37), residues: 132 loop : -0.77 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 9 TYR 0.013 0.001 TYR A 70 PHE 0.015 0.001 PHE F 120 TRP 0.010 0.001 TRP E 250 HIS 0.008 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00324 (43320) covalent geometry : angle 0.61735 (62760) hydrogen bonds : bond 0.08535 ( 1398) hydrogen bonds : angle 3.97285 ( 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 61 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 1.153 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 61 average time/residue: 0.7633 time to fit residues: 58.2049 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 : 1.438 ------------------------------------------------------------------------------- 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: 0.0000 chunk 355 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.052000 restraints weight = 105033.206| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.04 r_work: 0.2669 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43320 Z= 0.168 Angle : 0.593 10.496 62760 Z= 0.312 Chirality : 0.039 0.286 7734 Planarity : 0.004 0.043 4842 Dihedral : 25.291 178.130 16452 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.94 % Allowed : 15.86 % Favored : 82.20 % 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: 1.55 (0.16), residues: 2940 helix: 2.51 (0.13), residues: 1500 sheet: 0.32 (0.36), residues: 132 loop : -0.70 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 9 TYR 0.016 0.001 TYR F 70 PHE 0.017 0.001 PHE D 120 TRP 0.012 0.001 TRP F 250 HIS 0.009 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00361 (43320) covalent geometry : angle 0.59306 (62760) hydrogen bonds : bond 0.09439 ( 1398) hydrogen bonds : angle 3.87856 ( 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 74 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 33 time to evaluate : 1.451 Fit side-chains outliers start: 41 outliers final: 14 residues processed: 72 average time/residue: 0.6333 time to fit residues: 59.4345 Evaluate side-chains 47 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 162 THR 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 162 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 162 THR 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: 2.9990 chunk 51 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 290 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052470 restraints weight = 104324.646| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.02 r_work: 0.2708 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43320 Z= 0.162 Angle : 0.571 10.042 62760 Z= 0.296 Chirality : 0.038 0.254 7734 Planarity : 0.004 0.032 4842 Dihedral : 25.008 175.943 16452 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.09 % Allowed : 15.86 % Favored : 83.05 % 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: 1.74 (0.16), residues: 2940 helix: 2.69 (0.13), residues: 1506 sheet: 0.30 (0.36), residues: 132 loop : -0.66 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 143 TYR 0.013 0.001 TYR D 70 PHE 0.015 0.001 PHE C 120 TRP 0.012 0.001 TRP E 250 HIS 0.008 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00349 (43320) covalent geometry : angle 0.57101 (62760) hydrogen bonds : bond 0.08718 ( 1398) hydrogen bonds : angle 3.65168 ( 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 58 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 1.137 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 56 average time/residue: 0.6051 time to fit residues: 44.5913 Evaluate side-chains 43 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B 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 D residue 265 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 248 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: 2.9990 chunk 131 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 306 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 377 optimal weight: 8.9990 chunk 294 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.089970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053993 restraints weight = 104796.700| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.02 r_work: 0.2745 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 43320 Z= 0.123 Angle : 0.532 8.880 62760 Z= 0.275 Chirality : 0.036 0.239 7734 Planarity : 0.003 0.029 4842 Dihedral : 24.696 178.843 16452 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.76 % Allowed : 16.15 % Favored : 83.10 % 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: 2.03 (0.16), residues: 2940 helix: 2.96 (0.13), residues: 1506 sheet: 0.47 (0.36), residues: 132 loop : -0.56 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 9 TYR 0.011 0.001 TYR F 70 PHE 0.010 0.001 PHE A 120 TRP 0.012 0.001 TRP B 250 HIS 0.006 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00252 (43320) covalent geometry : angle 0.53242 (62760) hydrogen bonds : bond 0.07916 ( 1398) hydrogen bonds : angle 3.47911 ( 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 59 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 57 average time/residue: 0.8013 time to fit residues: 56.9453 Evaluate side-chains 53 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C 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 275 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 117 optimal weight: 0.0040 chunk 319 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 139 optimal weight: 0.0270 chunk 50 optimal weight: 8.9990 chunk 84 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 overall best weight: 0.9630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.090478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.054483 restraints weight = 105011.301| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.02 r_work: 0.2758 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43320 Z= 0.114 Angle : 0.516 8.130 62760 Z= 0.265 Chirality : 0.035 0.225 7734 Planarity : 0.003 0.049 4842 Dihedral : 24.625 177.192 16452 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.75 % Allowed : 15.01 % Favored : 83.24 % 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: 2.15 (0.16), residues: 2940 helix: 3.05 (0.13), residues: 1506 sheet: 0.62 (0.36), residues: 132 loop : -0.51 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 9 TYR 0.011 0.001 TYR A 329 PHE 0.010 0.001 PHE A 120 TRP 0.012 0.001 TRP A 250 HIS 0.006 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00229 (43320) covalent geometry : angle 0.51603 (62760) hydrogen bonds : bond 0.07515 ( 1398) hydrogen bonds : angle 3.38521 ( 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 77 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 40 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 75 average time/residue: 0.9375 time to fit residues: 84.0836 Evaluate side-chains 55 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C 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 162 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 359 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 chunk 353 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.088616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052259 restraints weight = 104489.447| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.04 r_work: 0.2667 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43320 Z= 0.158 Angle : 0.550 8.086 62760 Z= 0.284 Chirality : 0.036 0.243 7734 Planarity : 0.003 0.028 4842 Dihedral : 24.618 178.555 16452 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.42 % Allowed : 14.63 % Favored : 83.95 % 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: 2.07 (0.16), residues: 2940 helix: 2.99 (0.13), residues: 1506 sheet: 0.73 (0.36), residues: 132 loop : -0.56 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 242 TYR 0.013 0.001 TYR D 329 PHE 0.011 0.001 PHE C 120 TRP 0.012 0.001 TRP B 250 HIS 0.008 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00343 (43320) covalent geometry : angle 0.54955 (62760) hydrogen bonds : bond 0.08764 ( 1398) hydrogen bonds : angle 3.58281 ( 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 67 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 37 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 67 average time/residue: 0.7106 time to fit residues: 60.5750 Evaluate side-chains 57 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 247 THR 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: 2.9990 chunk 21 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.088843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.052525 restraints weight = 104257.206| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.02 r_work: 0.2675 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43320 Z= 0.142 Angle : 0.539 8.067 62760 Z= 0.279 Chirality : 0.036 0.240 7734 Planarity : 0.003 0.027 4842 Dihedral : 24.612 178.730 16452 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.23 % Allowed : 14.63 % Favored : 84.14 % 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: 2.06 (0.16), residues: 2940 helix: 2.99 (0.13), residues: 1506 sheet: 0.64 (0.35), residues: 132 loop : -0.57 (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 329 PHE 0.011 0.001 PHE B 120 TRP 0.012 0.001 TRP B 250 HIS 0.008 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00301 (43320) covalent geometry : angle 0.53909 (62760) hydrogen bonds : bond 0.08490 ( 1398) hydrogen bonds : angle 3.54641 ( 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 63 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 37 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 ARG cc_start: 0.8909 (ttm170) cc_final: 0.8585 (ttm170) REVERT: E 388 ARG cc_start: 0.8906 (ttm170) cc_final: 0.8575 (ttm170) outliers start: 26 outliers final: 21 residues processed: 61 average time/residue: 0.8206 time to fit residues: 61.6362 Evaluate side-chains 58 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 162 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 162 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 230 optimal weight: 0.0030 chunk 216 optimal weight: 0.4980 chunk 367 optimal weight: 10.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN E 27 ASN F 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055775 restraints weight = 106198.773| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.02 r_work: 0.2791 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 43320 Z= 0.101 Angle : 0.503 8.002 62760 Z= 0.257 Chirality : 0.034 0.209 7734 Planarity : 0.003 0.027 4842 Dihedral : 24.504 179.357 16452 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.71 % Allowed : 15.48 % Favored : 83.81 % 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: 2.29 (0.16), residues: 2940 helix: 3.17 (0.13), residues: 1500 sheet: 0.85 (0.38), residues: 132 loop : -0.44 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 367 TYR 0.010 0.001 TYR C 329 PHE 0.007 0.001 PHE A 120 TRP 0.010 0.001 TRP E 250 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00196 (43320) covalent geometry : angle 0.50329 (62760) hydrogen bonds : bond 0.06863 ( 1398) hydrogen bonds : angle 3.26917 ( 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 52 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 ARG cc_start: 0.8936 (ttm170) cc_final: 0.8685 (ttm170) REVERT: C 388 ARG cc_start: 0.8909 (ttm170) cc_final: 0.8449 (ttm170) REVERT: D 388 ARG cc_start: 0.8932 (ttm170) cc_final: 0.8673 (ttm170) REVERT: F 388 ARG cc_start: 0.8906 (ttm170) cc_final: 0.8444 (ttm170) outliers start: 15 outliers final: 11 residues processed: 49 average time/residue: 0.8764 time to fit residues: 52.2508 Evaluate side-chains 44 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR 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 C residue 162 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain F residue 162 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 356 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 166 optimal weight: 0.4980 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 354 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 364 optimal weight: 8.9990 chunk 123 optimal weight: 0.3980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.051795 restraints weight = 104216.203| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.02 r_work: 0.2654 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3047 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= 0.189 Angle : 0.563 8.211 62760 Z= 0.291 Chirality : 0.037 0.240 7734 Planarity : 0.003 0.039 4842 Dihedral : 24.565 178.949 16452 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.66 % Allowed : 15.44 % Favored : 83.90 % 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: 2.06 (0.16), residues: 2940 helix: 2.97 (0.13), residues: 1506 sheet: 0.66 (0.36), residues: 132 loop : -0.55 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 9 TYR 0.025 0.001 TYR E 390 PHE 0.012 0.001 PHE C 120 TRP 0.014 0.002 TRP E 250 HIS 0.009 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00421 (43320) covalent geometry : angle 0.56259 (62760) hydrogen bonds : bond 0.09160 ( 1398) hydrogen bonds : angle 3.64033 ( 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 51 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.8410 time to fit residues: 51.1851 Evaluate side-chains 46 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 72 SER 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: 2.9990 chunk 84 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 217 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.090230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054052 restraints weight = 105754.091| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.02 r_work: 0.2715 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 43320 Z= 0.115 Angle : 0.513 8.079 62760 Z= 0.264 Chirality : 0.035 0.219 7734 Planarity : 0.003 0.062 4842 Dihedral : 24.484 179.997 16452 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.24 % Allowed : 15.81 % Favored : 83.95 % 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: 2.19 (0.16), residues: 2940 helix: 3.10 (0.13), residues: 1506 sheet: 0.75 (0.37), residues: 132 loop : -0.51 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 9 TYR 0.025 0.001 TYR B 390 PHE 0.008 0.001 PHE D 120 TRP 0.011 0.001 TRP D 250 HIS 0.006 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00232 (43320) covalent geometry : angle 0.51316 (62760) hydrogen bonds : bond 0.07561 ( 1398) hydrogen bonds : angle 3.39872 ( 3642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12036.97 seconds wall clock time: 205 minutes 49.13 seconds (12349.13 seconds total)