Starting phenix.real_space_refine on Mon Jul 6 22:04:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nlv_49523/07_2026/9nlv_49523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nlv_49523/07_2026/9nlv_49523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nlv_49523/07_2026/9nlv_49523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nlv_49523/07_2026/9nlv_49523.map" model { file = "/net/cci-nas-00/data/ceres_data/9nlv_49523/07_2026/9nlv_49523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nlv_49523/07_2026/9nlv_49523.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 846 5.49 5 S 48 5.16 5 C 22860 2.51 5 N 7146 2.21 5 O 9780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40680 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "B" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "C" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "D" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "E" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "F" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3779 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 473} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 16, 'ASP:plan': 12, 'ASN:plan1': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "K" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Chain: "L" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 19, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 31, 'rna3p': 109} Time building chain proxies: 7.78, per 1000 atoms: 0.19 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: 3.42 Conformation dependent library (CDL) restraints added in 1.3 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: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER A 56 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.792A pdb=" N ILE A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.537A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 336 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS A 341 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'B' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER B 56 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.538A pdb=" N ALA B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.563A pdb=" N PHE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 262 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.775A pdb=" N LYS B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 370 removed outlier: 3.530A pdb=" N LEU B 359 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 403 through 432 removed outlier: 3.601A pdb=" N LEU B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 468 through 484 removed outlier: 3.780A pdb=" N ILE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 482 " --> pdb=" O LYS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'C' and resid 2 through 41 removed outlier: 3.666A pdb=" N GLN C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 27 " --> pdb=" O HIS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER C 56 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 69 through 83 removed outlier: 3.792A pdb=" N ILE C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.538A pdb=" N ALA C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 272 removed outlier: 3.740A pdb=" N PHE C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 336 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS C 341 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 454 Processing helix chain 'C' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 482 " --> pdb=" O LYS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'D' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN D 6 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 27 " --> pdb=" O HIS D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER D 56 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.538A pdb=" N ALA D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.758A pdb=" N LEU D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 272 removed outlier: 3.742A pdb=" N PHE D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 262 " --> pdb=" O CYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 336 Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS D 341 " --> pdb=" O PRO D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU D 359 " --> pdb=" O ASP D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'D' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'D' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 482 " --> pdb=" O LYS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'E' and resid 2 through 41 removed outlier: 3.667A pdb=" N GLN E 6 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN E 27 " --> pdb=" O HIS E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 44 No H-bonds generated for 'chain 'E' and resid 42 through 44' Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER E 56 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 124 " --> pdb=" O PHE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 144 through 159 removed outlier: 3.537A pdb=" N ALA E 148 " --> pdb=" O ASN E 144 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS E 158 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 193 through 203 removed outlier: 3.562A pdb=" N PHE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN E 262 " --> pdb=" O CYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 336 Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS E 341 " --> pdb=" O PRO E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU E 359 " --> pdb=" O ASP E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 383 Processing helix chain 'E' and resid 393 through 398 Processing helix chain 'E' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 447 No H-bonds generated for 'chain 'E' and resid 445 through 447' Processing helix chain 'E' and resid 448 through 454 Processing helix chain 'E' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN E 481 " --> pdb=" O GLN E 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 482 " --> pdb=" O LYS E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 489 Processing helix chain 'F' and resid 2 through 41 removed outlier: 3.666A pdb=" N GLN F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN F 27 " --> pdb=" O HIS F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 44 No H-bonds generated for 'chain 'F' and resid 42 through 44' Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.811A pdb=" N SER F 56 " --> pdb=" O ASN F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 61 Processing helix chain 'F' and resid 62 through 69 Processing helix chain 'F' and resid 69 through 83 removed outlier: 3.793A pdb=" N ILE F 73 " --> pdb=" O ASN F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 129 removed outlier: 3.695A pdb=" N ARG F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 124 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.537A pdb=" N ALA F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 193 through 203 removed outlier: 3.563A pdb=" N PHE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 removed outlier: 3.759A pdb=" N LEU F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 237 removed outlier: 3.719A pdb=" N GLY F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 272 removed outlier: 3.741A pdb=" N PHE F 261 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN F 262 " --> pdb=" O CYS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 336 Processing helix chain 'F' and resid 337 through 341 removed outlier: 3.776A pdb=" N LYS F 341 " --> pdb=" O PRO F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 370 removed outlier: 3.529A pdb=" N LEU F 359 " --> pdb=" O ASP F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 383 Processing helix chain 'F' and resid 393 through 398 Processing helix chain 'F' and resid 403 through 432 removed outlier: 3.600A pdb=" N LEU F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 447 No H-bonds generated for 'chain 'F' and resid 445 through 447' Processing helix chain 'F' and resid 448 through 454 Processing helix chain 'F' and resid 468 through 484 removed outlier: 3.781A pdb=" N ILE F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN F 481 " --> pdb=" O GLN F 477 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 482 " --> pdb=" O LYS F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR A 247 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 167 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS A 298 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 285 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS A 274 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR B 247 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE B 167 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS B 298 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 285 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 4.719A pdb=" N LYS B 274 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA7, first strand: chain 'C' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR C 247 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE C 167 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS C 298 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 285 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS C 274 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'D' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR D 247 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE D 167 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LYS D 298 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 285 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS D 274 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 301 through 303 Processing sheet with id=AB4, first strand: chain 'E' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR E 247 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE E 167 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS E 298 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU E 285 " --> pdb=" O LYS E 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.719A pdb=" N LYS E 274 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 301 through 303 Processing sheet with id=AB7, first strand: chain 'F' and resid 239 through 243 removed outlier: 4.422A pdb=" N THR F 247 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE F 167 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS F 298 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU F 285 " --> pdb=" O LYS F 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 169 through 170 removed outlier: 4.720A pdb=" N LYS F 274 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 303 1212 hydrogen bonds defined for protein. 3438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 186 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 420 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 4.49 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: 0.12 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: 14.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 37.090 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 43320 Z= 0.256 Angle : 0.713 6.960 62760 Z= 0.534 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/Z covalent geometry : bond 0.00380 / 0.26 (43320) covalent geometry : angle 0.71261 / 0.53 (62760) hydrogen bonds : bond 0.21600 / 14.39 ( 1398) hydrogen bonds : angle 6.68930 / 4.83 ( 3642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.8955 time to fit residues: 49.3222 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 : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0030 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.089633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.054283 restraints weight = 105676.420| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.07 r_work: 0.2735 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43320 Z= 0.153 Angle : 0.557 9.852 62760 Z= 0.334 Chirality : 0.042 0.354 7734 Planarity : 0.004 0.036 4842 Dihedral : 26.299 175.783 16452 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.57 % Allowed : 17.52 % Favored : 81.91 % 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: 0.96 (0.15), residues: 2940 helix: 1.83 (0.13), residues: 1494 sheet: 0.27 (0.36), residues: 132 loop : -0.74 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 9 TYR 0.014 0.001 TYR D 70 PHE 0.011 0.001 PHE F 120 TRP 0.011 0.002 TRP E 250 HIS 0.009 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (43320) covalent geometry : angle 0.55700 / 0.33 (62760) hydrogen bonds : bond 0.09643 / 6.53 ( 1398) hydrogen bonds : angle 4.19775 / 3.00 ( 3642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.988 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 0.5963 time to fit residues: 41.2693 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 : 1.213 ------------------------------------------------------------------------------- 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: 0.0040 chunk 355 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 0.0050 chunk 141 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.089173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053490 restraints weight = 106015.863| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.06 r_work: 0.2725 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 43320 Z= 0.144 Angle : 0.499 10.476 62760 Z= 0.297 Chirality : 0.039 0.243 7734 Planarity : 0.004 0.072 4842 Dihedral : 25.687 179.389 16452 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.80 % Allowed : 16.34 % Favored : 81.87 % 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: 1.60 (0.16), residues: 2940 helix: 2.52 (0.13), residues: 1506 sheet: 0.43 (0.34), residues: 132 loop : -0.66 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 9 TYR 0.014 0.001 TYR F 70 PHE 0.015 0.002 PHE A 120 TRP 0.010 0.001 TRP E 250 HIS 0.011 0.002 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (43320) covalent geometry : angle 0.49900 / 0.30 (62760) hydrogen bonds : bond 0.09172 / 6.21 ( 1398) hydrogen bonds : angle 3.79646 / 2.73 ( 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 78 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 40 time to evaluate : 1.174 Fit side-chains outliers start: 38 outliers final: 10 residues processed: 76 average time/residue: 0.5835 time to fit residues: 57.9130 Evaluate side-chains 45 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 247 THR 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: 0.1980 chunk 51 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 356 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 313 optimal weight: 9.9990 chunk 290 optimal weight: 0.6980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.089377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.053471 restraints weight = 104927.381| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.02 r_work: 0.2707 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1904 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= 0.136 Angle : 0.492 10.647 62760 Z= 0.291 Chirality : 0.039 0.272 7734 Planarity : 0.003 0.026 4842 Dihedral : 25.409 177.696 16452 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.85 % Allowed : 16.00 % Favored : 83.14 % 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: 1.79 (0.16), residues: 2940 helix: 2.69 (0.13), residues: 1506 sheet: 0.28 (0.33), residues: 132 loop : -0.56 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 9 TYR 0.013 0.001 TYR A 329 PHE 0.012 0.001 PHE D 120 TRP 0.012 0.001 TRP B 250 HIS 0.009 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (43320) covalent geometry : angle 0.49197 / 0.29 (62760) hydrogen bonds : bond 0.08505 / 5.73 ( 1398) hydrogen bonds : angle 3.62370 / 2.60 ( 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 51 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 33 time to evaluate : 1.258 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 49 average time/residue: 0.6146 time to fit residues: 39.5618 Evaluate side-chains 43 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 221 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 306 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 377 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052103 restraints weight = 104705.511| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.04 r_work: 0.2670 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43320 Z= 0.158 Angle : 0.502 10.252 62760 Z= 0.295 Chirality : 0.039 0.252 7734 Planarity : 0.004 0.046 4842 Dihedral : 25.200 178.834 16452 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.47 % Allowed : 15.34 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.16), residues: 2940 helix: 2.84 (0.13), residues: 1506 sheet: 0.39 (0.35), residues: 132 loop : -0.60 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 9 TYR 0.013 0.001 TYR D 329 PHE 0.016 0.001 PHE C 120 TRP 0.014 0.001 TRP B 250 HIS 0.009 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (43320) covalent geometry : angle 0.50221 / 0.29 (62760) hydrogen bonds : bond 0.09365 / 6.30 ( 1398) hydrogen bonds : angle 3.71342 / 2.67 ( 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 64 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 33 time to evaluate : 1.150 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 62 average time/residue: 0.4628 time to fit residues: 39.9128 Evaluate side-chains 44 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 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 247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 319 optimal weight: 10.0000 chunk 343 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 139 optimal weight: 0.0010 chunk 50 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.087972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.051613 restraints weight = 104662.130| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.04 r_work: 0.2656 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43320 Z= 0.168 Angle : 0.511 10.058 62760 Z= 0.300 Chirality : 0.040 0.284 7734 Planarity : 0.003 0.033 4842 Dihedral : 25.102 178.177 16452 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.37 % Allowed : 15.01 % Favored : 83.62 % 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: 1.82 (0.16), residues: 2940 helix: 2.79 (0.13), residues: 1506 sheet: 0.30 (0.34), residues: 132 loop : -0.67 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 161 TYR 0.013 0.001 TYR F 70 PHE 0.014 0.001 PHE F 120 TRP 0.013 0.002 TRP F 250 HIS 0.009 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (43320) covalent geometry : angle 0.51129 / 0.30 (62760) hydrogen bonds : bond 0.09378 / 6.30 ( 1398) hydrogen bonds : angle 3.71579 / 2.67 ( 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 60 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 31 time to evaluate : 1.107 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 56 average time/residue: 0.4868 time to fit residues: 37.1820 Evaluate side-chains 51 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 B residue 162 THR Chi-restraints excluded: chain B residue 265 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 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 265 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 359 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 353 optimal weight: 30.0000 chunk 184 optimal weight: 0.0170 chunk 63 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.090217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054320 restraints weight = 104691.978| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.03 r_work: 0.2756 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2502 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= 0.108 Angle : 0.453 9.520 62760 Z= 0.270 Chirality : 0.036 0.241 7734 Planarity : 0.003 0.022 4842 Dihedral : 24.990 179.441 16452 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.90 % Allowed : 15.20 % 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: 2.02 (0.16), residues: 2940 helix: 2.98 (0.13), residues: 1506 sheet: 0.45 (0.35), residues: 132 loop : -0.59 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 143 TYR 0.011 0.001 TYR A 329 PHE 0.008 0.001 PHE A 440 TRP 0.011 0.001 TRP D 250 HIS 0.004 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.11 (43320) covalent geometry : angle 0.45258 / 0.27 (62760) hydrogen bonds : bond 0.07720 / 5.17 ( 1398) hydrogen bonds : angle 3.45974 / 2.49 ( 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 54 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 54 average time/residue: 0.5782 time to fit residues: 41.1196 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 : 1.127 ------------------------------------------------------------------------------- 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 248 ILE 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 C residue 248 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 235 optimal weight: 0.7980 chunk 297 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 334 optimal weight: 20.0000 chunk 287 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.052007 restraints weight = 103935.984| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.03 r_work: 0.2690 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 43320 Z= 0.169 Angle : 0.494 9.368 62760 Z= 0.289 Chirality : 0.039 0.260 7734 Planarity : 0.003 0.036 4842 Dihedral : 24.956 178.604 16452 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.90 % Allowed : 15.10 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.16), residues: 2940 helix: 2.92 (0.13), residues: 1506 sheet: 0.37 (0.35), residues: 132 loop : -0.63 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 9 TYR 0.014 0.001 TYR A 306 PHE 0.014 0.001 PHE C 120 TRP 0.013 0.001 TRP F 250 HIS 0.009 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (43320) covalent geometry : angle 0.49432 / 0.29 (62760) hydrogen bonds : bond 0.09166 / 6.15 ( 1398) hydrogen bonds : angle 3.65273 / 2.62 ( 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 52 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 52 average time/residue: 0.6594 time to fit residues: 43.8102 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 : 1.013 ------------------------------------------------------------------------------- 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 275 ILE 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 6 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 230 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 367 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 222 optimal weight: 0.0170 chunk 241 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.088836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.052527 restraints weight = 104668.741| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.03 r_work: 0.2703 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43320 Z= 0.135 Angle : 0.475 9.217 62760 Z= 0.280 Chirality : 0.038 0.256 7734 Planarity : 0.003 0.026 4842 Dihedral : 24.947 178.936 16452 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.90 % Allowed : 14.91 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.16), residues: 2940 helix: 2.98 (0.13), residues: 1506 sheet: 0.38 (0.36), residues: 132 loop : -0.64 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 84 TYR 0.012 0.001 TYR A 306 PHE 0.010 0.001 PHE C 120 TRP 0.013 0.001 TRP B 250 HIS 0.008 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (43320) covalent geometry : angle 0.47511 / 0.28 (62760) hydrogen bonds : bond 0.08673 / 5.82 ( 1398) hydrogen bonds : angle 3.58246 / 2.57 ( 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: 19 poor density : 33 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 52 average time/residue: 0.5985 time to fit residues: 40.0266 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 : 1.141 ------------------------------------------------------------------------------- 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 248 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 248 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 356 optimal weight: 30.0000 chunk 315 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 354 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.088746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.052483 restraints weight = 104273.118| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.03 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: 0.8589 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43320 Z= 0.138 Angle : 0.473 7.778 62760 Z= 0.279 Chirality : 0.038 0.259 7734 Planarity : 0.003 0.029 4842 Dihedral : 24.797 179.897 16452 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.57 % Allowed : 15.06 % Favored : 84.38 % 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: 1.93 (0.16), residues: 2940 helix: 2.91 (0.13), residues: 1506 sheet: 0.40 (0.36), residues: 132 loop : -0.65 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 367 TYR 0.014 0.001 TYR E 306 PHE 0.013 0.001 PHE C 120 TRP 0.010 0.001 TRP C 250 HIS 0.008 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (43320) covalent geometry : angle 0.47322 / 0.28 (62760) hydrogen bonds : bond 0.08700 / 5.84 ( 1398) hydrogen bonds : angle 3.58912 / 2.58 ( 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 49 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 0.7161 time to fit residues: 43.2838 Evaluate side-chains 42 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain F residue 247 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 248 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.086818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.050214 restraints weight = 104786.906| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.05 r_work: 0.2613 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 43320 Z= 0.241 Angle : 0.548 7.791 62760 Z= 0.319 Chirality : 0.041 0.285 7734 Planarity : 0.004 0.045 4842 Dihedral : 24.849 179.919 16452 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.76 % Allowed : 14.77 % Favored : 84.47 % 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: 1.68 (0.16), residues: 2940 helix: 2.69 (0.13), residues: 1506 sheet: 0.22 (0.34), residues: 132 loop : -0.74 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 140 TYR 0.017 0.002 TYR A 306 PHE 0.017 0.002 PHE C 120 TRP 0.014 0.002 TRP E 250 HIS 0.011 0.002 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (43320) covalent geometry : angle 0.54756 / 0.32 (62760) hydrogen bonds : bond 0.10620 / 7.12 ( 1398) hydrogen bonds : angle 3.88087 / 2.79 ( 3642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10660.75 seconds wall clock time: 182 minutes 40.02 seconds (10960.02 seconds total)