Starting phenix.real_space_refine on Fri Aug 7 13:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ash_43814/08_2026/9ash_43814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ash_43814/08_2026/9ash_43814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ash_43814/08_2026/9ash_43814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ash_43814/08_2026/9ash_43814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ash_43814/08_2026/9ash_43814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ash_43814/08_2026/9ash_43814.map" } resolution = 2.58 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= 0.134 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: 6 Type Number sf(0) Gaussians P 66 5.49 5 Mg 3 5.21 5 S 53 5.16 5 C 13950 2.51 5 N 3799 2.21 5 O 4438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22309 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6078 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 743} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2401 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 10, 'TRANS': 286} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1620 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1676 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1676 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1676 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 792 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 11, 'rna3p_pyr': 7} Link IDs: {'rna2p': 19, 'rna3p': 17} Chain: "D" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain: "E" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1094 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 467 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 20} Chain: "C" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 134} Chain: "J" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2506 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'ATP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, None: 1} Not linked: pdbres="ATP P 1 " pdbres=" A P 2 " Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' MG': 3, 'ATP': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 4.98, per 1000 atoms: 0.22 Number of scatterers: 22309 At special positions: 0 Unit cell: (95.586, 122.436, 207.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 66 15.00 Mg 3 11.99 O 4438 8.00 N 3799 7.00 C 13950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 405 " distance=2.02 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.02 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 31 sheets defined 44.6% alpha, 14.8% beta 15 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.530A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 21 removed outlier: 4.120A pdb=" N ILE A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 72 through 85 removed outlier: 3.692A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.687A pdb=" N VAL A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.635A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 202 through 225 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 271 through 295 removed outlier: 4.449A pdb=" N ALA A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 317 through 339 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 364 through 381 removed outlier: 4.326A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.670A pdb=" N GLN A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 4.225A pdb=" N LEU A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 538 through 564 removed outlier: 4.030A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.020A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 637 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.670A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 removed outlier: 3.786A pdb=" N ALA A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 707 through 721 Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 739 through 754 Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.564A pdb=" N GLU B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 removed outlier: 4.183A pdb=" N TYR B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.663A pdb=" N LEU B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'F' and resid 22 through 27 Processing helix chain 'F' and resid 45 through 63 Processing helix chain 'F' and resid 74 through 82 removed outlier: 3.945A pdb=" N LEU F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 removed outlier: 3.630A pdb=" N THR F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 204 through 213 removed outlier: 3.500A pdb=" N LEU F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 63 removed outlier: 3.846A pdb=" N ASN H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.654A pdb=" N ASP H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.635A pdb=" N PHE H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 174 Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 157 through 174 Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.534A pdb=" N LEU G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 69 through 73 removed outlier: 3.517A pdb=" N ASP I 73 " --> pdb=" O PRO I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 Processing helix chain 'I' and resid 103 through 110 Processing helix chain 'I' and resid 155 through 157 No H-bonds generated for 'chain 'I' and resid 155 through 157' Processing helix chain 'I' and resid 158 through 174 removed outlier: 3.628A pdb=" N PHE I 174 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 removed outlier: 3.535A pdb=" N LEU I 208 " --> pdb=" O LYS I 204 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 40 Processing helix chain 'D' and resid 57 through 73 removed outlier: 3.798A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 147 removed outlier: 3.556A pdb=" N PHE D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 40 Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 57 through 73 removed outlier: 4.257A pdb=" N ASN E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.814A pdb=" N GLU E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 125 through 147 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 57 through 73 Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.681A pdb=" N ASP C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 removed outlier: 3.854A pdb=" N PHE C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 125 through 144 Processing helix chain 'J' and resid 41 through 52 Processing helix chain 'J' and resid 54 through 60 Processing helix chain 'J' and resid 68 through 73 removed outlier: 3.605A pdb=" N VAL J 73 " --> pdb=" O TYR J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 140 removed outlier: 4.126A pdb=" N ALA J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 3.751A pdb=" N ALA J 154 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 150 through 155' Processing helix chain 'J' and resid 165 through 167 No H-bonds generated for 'chain 'J' and resid 165 through 167' Processing helix chain 'J' and resid 209 through 226 Processing helix chain 'J' and resid 228 through 237 Processing helix chain 'J' and resid 276 through 280 Processing helix chain 'J' and resid 287 through 303 removed outlier: 3.650A pdb=" N LEU J 302 " --> pdb=" O ILE J 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 305 removed outlier: 5.981A pdb=" N ILE A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 313 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 305 removed outlier: 5.981A pdb=" N ILE A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 313 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412 removed outlier: 5.284A pdb=" N ILE A 417 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.629A pdb=" N LYS A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 473 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 583 removed outlier: 4.148A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.531A pdb=" N THR B 153 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE B 8 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.705A pdb=" N LYS B 58 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 160 " --> pdb=" O LYS B 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 132 Processing sheet with id=AB1, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB3, first strand: chain 'B' and resid 272 through 277 removed outlier: 6.317A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 94 through 95 removed outlier: 6.866A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 123 Processing sheet with id=AB7, first strand: chain 'F' and resid 183 through 184 removed outlier: 7.669A pdb=" N GLY F 184 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE G 96 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN G 97 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU G 147 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR G 8 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN G 192 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL G 10 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE G 190 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 188 through 197 removed outlier: 5.626A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 7 " --> pdb=" O PHE H 146 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLU H 147 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN H 97 " --> pdb=" O GLU H 147 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY G 184 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE H 96 " --> pdb=" O GLY G 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'H' and resid 115 through 124 removed outlier: 3.564A pdb=" N VAL H 129 " --> pdb=" O ASN H 124 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 183 through 184 removed outlier: 4.401A pdb=" N ASN I 97 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU I 147 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY I 7 " --> pdb=" O PHE I 146 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR I 8 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN I 192 " --> pdb=" O THR I 8 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL I 10 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE I 190 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=AC5, first strand: chain 'G' and resid 115 through 123 Processing sheet with id=AC6, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'I' and resid 115 through 123 Processing sheet with id=AC8, first strand: chain 'I' and resid 183 through 184 removed outlier: 5.313A pdb=" N THR J 200 " --> pdb=" O SER J 159 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE J 203 " --> pdb=" O LYS J 3 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AD1, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.954A pdb=" N PHE D 42 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 18 through 22 removed outlier: 4.073A pdb=" N GLY J 20 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP J 112 " --> pdb=" O TYR J 187 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLU J 189 " --> pdb=" O ASP J 112 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN J 114 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU J 191 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N PHE J 116 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 28 through 31 Processing sheet with id=AD4, first strand: chain 'J' and resid 314 through 315 removed outlier: 3.571A pdb=" N LEU J 340 " --> pdb=" O ASP J 315 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7193 1.35 - 1.49: 5952 1.49 - 1.63: 9557 1.63 - 1.76: 10 1.76 - 1.90: 99 Bond restraints: 22811 Sorted by residual: bond pdb=" C1' ATP P 1 " pdb=" C2' ATP P 1 " ideal model delta sigma weight residual 1.531 1.308 0.223 1.20e-02 6.94e+03 3.46e+02 bond pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " ideal model delta sigma weight residual 1.531 1.308 0.223 1.20e-02 6.94e+03 3.45e+02 bond pdb=" C3' ATP P 1 " pdb=" C4' ATP P 1 " ideal model delta sigma weight residual 1.526 1.340 0.186 1.10e-02 8.26e+03 2.87e+02 bond pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " ideal model delta sigma weight residual 1.526 1.341 0.185 1.10e-02 8.26e+03 2.82e+02 bond pdb=" C1' ATP P 1 " pdb=" O4' ATP P 1 " ideal model delta sigma weight residual 1.416 1.582 -0.166 1.30e-02 5.92e+03 1.64e+02 ... (remaining 22806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 30921 3.95 - 7.90: 85 7.90 - 11.85: 5 11.85 - 15.80: 2 15.80 - 19.75: 2 Bond angle restraints: 31015 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 123.25 16.62 1.00e+00 1.00e+00 2.76e+02 angle pdb=" PB ATP P 1 " pdb=" O3B ATP P 1 " pdb=" PG ATP P 1 " ideal model delta sigma weight residual 139.87 124.93 14.94 1.00e+00 1.00e+00 2.23e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 124.23 12.60 1.00e+00 1.00e+00 1.59e+02 angle pdb=" PA ATP P 1 " pdb=" O3A ATP P 1 " pdb=" PB ATP P 1 " ideal model delta sigma weight residual 136.83 125.23 11.60 1.00e+00 1.00e+00 1.35e+02 angle pdb=" O4' G R 21 " pdb=" C1' G R 21 " pdb=" N9 G R 21 " ideal model delta sigma weight residual 108.20 115.19 -6.99 8.00e-01 1.56e+00 7.63e+01 ... (remaining 31010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 13449 34.73 - 69.45: 385 69.45 - 104.18: 52 104.18 - 138.91: 4 138.91 - 173.63: 2 Dihedral angle restraints: 13892 sinusoidal: 6276 harmonic: 7616 Sorted by residual: dihedral pdb=" O4' U T 8 " pdb=" C1' U T 8 " pdb=" N1 U T 8 " pdb=" C2 U T 8 " ideal model delta sinusoidal sigma weight residual 200.00 61.93 138.07 1 1.50e+01 4.44e-03 7.44e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual 93.00 19.96 73.04 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS A 405 " pdb=" SG CYS A 405 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual -86.00 -151.61 65.61 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 13889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2985 0.062 - 0.124: 448 0.124 - 0.186: 65 0.186 - 0.248: 5 0.248 - 0.310: 5 Chirality restraints: 3508 Sorted by residual: chirality pdb=" C1' G R 21 " pdb=" O4' G R 21 " pdb=" C2' G R 21 " pdb=" N9 G R 21 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C1' C R 15 " pdb=" O4' C R 15 " pdb=" C2' C R 15 " pdb=" N1 C R 15 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3505 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C R 15 " -0.045 2.00e-02 2.50e+03 2.39e-02 1.29e+01 pdb=" N1 C R 15 " 0.053 2.00e-02 2.50e+03 pdb=" C2 C R 15 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C R 15 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C R 15 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C R 15 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C R 15 " -0.015 2.00e-02 2.50e+03 pdb=" C5 C R 15 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C R 15 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R 21 " -0.048 2.00e-02 2.50e+03 2.05e-02 1.27e+01 pdb=" N9 G R 21 " 0.049 2.00e-02 2.50e+03 pdb=" C8 G R 21 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G R 21 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G R 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G R 21 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G R 21 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G R 21 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G R 21 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G R 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G R 21 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G R 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 19 " 0.032 2.00e-02 2.50e+03 1.65e-02 6.14e+00 pdb=" N1 C R 19 " -0.035 2.00e-02 2.50e+03 pdb=" C2 C R 19 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C R 19 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C R 19 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C R 19 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C R 19 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C R 19 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C R 19 " -0.004 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 193 2.55 - 3.14: 17507 3.14 - 3.73: 36037 3.73 - 4.31: 53572 4.31 - 4.90: 87544 Nonbonded interactions: 194853 Sorted by model distance: nonbonded pdb=" OD1 ASP A 520 " pdb="MG MG A 803 " model vdw 1.963 2.170 nonbonded pdb=" O VAL A 521 " pdb="MG MG A 803 " model vdw 1.998 2.170 nonbonded pdb=" OD1 ASP A 577 " pdb="MG MG A 802 " model vdw 2.010 2.170 nonbonded pdb=" O2G ATP P 1 " pdb="MG MG A 803 " model vdw 2.020 2.170 nonbonded pdb=" O1B ATP P 1 " pdb="MG MG A 803 " model vdw 2.024 2.170 ... (remaining 194848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 12 through 43 or (resid 44 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 149)) selection = (chain 'D' and (resid 12 through 43 or (resid 44 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 149)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 65 or resid 73 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.650 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.005 0.223 22816 Z= 0.370 Angle : 0.670 19.750 31023 Z= 0.451 Chirality : 0.046 0.310 3508 Planarity : 0.003 0.032 3755 Dihedral : 16.628 173.634 8980 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.64 (0.16), residues: 2594 helix: 0.82 (0.16), residues: 1096 sheet: -0.43 (0.25), residues: 388 loop : -1.71 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.013 0.001 TYR B 186 PHE 0.018 0.001 PHE A 553 TRP 0.009 0.001 TRP A 334 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.37 (22811) covalent geometry : angle 0.65933 / 0.45 (31015) SS BOND : bond 0.01033 / 0.52 ( 4) SS BOND : angle 7.59364 / 4.14 ( 8) hydrogen bonds : bond 0.16126 / 10.58 ( 1013) hydrogen bonds : angle 7.13552 / 4.95 ( 2929) Misc. bond : bond 0.04155 / 2.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8544 (tpp) cc_final: 0.8222 (tpp) REVERT: E 137 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7237 (mt-10) REVERT: C 134 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8409 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.5744 time to fit residues: 228.9291 Evaluate side-chains 267 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 176 ASN A 251 ASN A 381 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 460 GLN A 484 ASN A 526 GLN A 530 ASN A 555 ASN A 680 ASN A 709 ASN B 55 ASN B 134 HIS B 267 ASN F 62 ASN F 74 GLN F 131 ASN H 124 ASN H 180 HIS G 16 HIS G 111 ASN I 72 ASN I 134 GLN I 206 ASN D 50 GLN E 25 ASN E 65 ASN C 39 HIS C 73 ASN C 82 ASN C 123 GLN J 38 HIS J 65 HIS ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN J 301 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131196 restraints weight = 23606.074| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.97 r_work: 0.3320 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 22816 Z= 0.253 Angle : 0.682 20.742 31023 Z= 0.370 Chirality : 0.048 0.396 3508 Planarity : 0.005 0.056 3755 Dihedral : 15.026 171.277 3832 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.52 % Favored : 93.45 % Rotamer: Outliers : 1.81 % Allowed : 10.31 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.72 (0.16), residues: 2594 helix: 0.75 (0.16), residues: 1106 sheet: -0.48 (0.26), residues: 389 loop : -1.76 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 21 TYR 0.024 0.002 TYR A 458 PHE 0.026 0.002 PHE A 553 TRP 0.008 0.002 TRP A 334 HIS 0.008 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (22811) covalent geometry : angle 0.66798 / 0.36 (31015) SS BOND : bond 0.01674 / 0.84 ( 4) SS BOND : angle 8.46178 / 4.76 ( 8) hydrogen bonds : bond 0.05223 / 3.49 ( 1013) hydrogen bonds : angle 5.71531 / 3.98 ( 2929) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7018 (pp20) REVERT: A 161 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: A 171 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: A 243 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7655 (t0) REVERT: A 249 MET cc_start: 0.8647 (tpp) cc_final: 0.8342 (tpp) REVERT: A 683 LYS cc_start: 0.7341 (pmtt) cc_final: 0.6983 (pmtt) REVERT: B 135 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8134 (t0) REVERT: F 74 GLN cc_start: 0.7730 (tp40) cc_final: 0.7447 (tp-100) REVERT: H 180 HIS cc_start: 0.9071 (OUTLIER) cc_final: 0.8547 (m170) REVERT: G 53 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8807 (ttp) REVERT: G 153 ASP cc_start: 0.7881 (m-30) cc_final: 0.7601 (m-30) REVERT: G 159 GLU cc_start: 0.7861 (mm-30) cc_final: 0.6965 (pm20) REVERT: J 36 VAL cc_start: 0.4751 (t) cc_final: 0.4326 (p) outliers start: 41 outliers final: 22 residues processed: 299 average time/residue: 0.5830 time to fit residues: 199.8006 Evaluate side-chains 281 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 261 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 ASN A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 646 GLN F 62 ASN H 180 HIS I 134 GLN I 180 HIS E 22 ASN C 25 ASN C 75 ASN C 82 ASN J 42 HIS ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137210 restraints weight = 23599.523| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.74 r_work: 0.3384 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 22816 Z= 0.135 Angle : 0.569 19.493 31023 Z= 0.313 Chirality : 0.043 0.380 3508 Planarity : 0.004 0.049 3755 Dihedral : 14.961 170.647 3832 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.87 % Rotamer: Outliers : 1.81 % Allowed : 12.21 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.55 (0.16), residues: 2594 helix: 0.97 (0.16), residues: 1106 sheet: -0.51 (0.25), residues: 389 loop : -1.71 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.015 0.001 TYR E 135 PHE 0.022 0.001 PHE E 26 TRP 0.007 0.001 TRP A 334 HIS 0.011 0.001 HIS H 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (22811) covalent geometry : angle 0.55526 / 0.31 (31015) SS BOND : bond 0.01262 / 0.63 ( 4) SS BOND : angle 7.66962 / 4.36 ( 8) hydrogen bonds : bond 0.04255 / 2.83 ( 1013) hydrogen bonds : angle 5.35288 / 3.74 ( 2929) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7077 (pp20) REVERT: A 171 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: A 249 MET cc_start: 0.8596 (tpp) cc_final: 0.8302 (tpp) REVERT: A 488 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7673 (ttp-110) REVERT: B 200 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7443 (mt-10) REVERT: F 74 GLN cc_start: 0.7794 (tp40) cc_final: 0.7450 (tp40) REVERT: G 159 GLU cc_start: 0.7824 (mm-30) cc_final: 0.6983 (pm20) REVERT: G 160 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7075 (mtpt) REVERT: I 176 TYR cc_start: 0.8433 (p90) cc_final: 0.8165 (p90) REVERT: C 101 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7490 (pt0) REVERT: C 124 ARG cc_start: 0.7563 (mtt90) cc_final: 0.6845 (mtp-110) REVERT: C 134 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7977 (mtm-85) REVERT: J 36 VAL cc_start: 0.4676 (t) cc_final: 0.4236 (p) REVERT: J 162 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5382 (mm-30) outliers start: 41 outliers final: 14 residues processed: 306 average time/residue: 0.5775 time to fit residues: 203.7107 Evaluate side-chains 276 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain C residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 45 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.0170 chunk 184 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN A 646 GLN F 62 ASN I 134 GLN C 25 ASN C 75 ASN C 82 ASN ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.177686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137091 restraints weight = 23458.980| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.79 r_work: 0.3363 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 22816 Z= 0.151 Angle : 0.573 19.483 31023 Z= 0.314 Chirality : 0.043 0.387 3508 Planarity : 0.004 0.043 3755 Dihedral : 14.899 170.699 3832 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 2.35 % Allowed : 13.41 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.48 (0.16), residues: 2594 helix: 1.04 (0.16), residues: 1109 sheet: -0.41 (0.26), residues: 380 loop : -1.73 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.021 0.001 TYR A 458 PHE 0.027 0.001 PHE E 26 TRP 0.006 0.001 TRP A 334 HIS 0.005 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (22811) covalent geometry : angle 0.55898 / 0.31 (31015) SS BOND : bond 0.01326 / 0.66 ( 4) SS BOND : angle 7.83863 / 4.41 ( 8) hydrogen bonds : bond 0.04146 / 2.76 ( 1013) hydrogen bonds : angle 5.22469 / 3.66 ( 2929) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7095 (pp20) REVERT: A 171 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: A 243 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7644 (t0) REVERT: A 249 MET cc_start: 0.8609 (tpp) cc_final: 0.8316 (tpp) REVERT: A 488 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.7745 (ttp-110) REVERT: A 686 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6212 (mt-10) REVERT: B 135 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.7994 (t0) REVERT: B 200 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7494 (mt-10) REVERT: F 74 GLN cc_start: 0.7831 (tp40) cc_final: 0.7522 (tp40) REVERT: H 154 ASP cc_start: 0.7579 (t0) cc_final: 0.7309 (t0) REVERT: H 180 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8609 (m170) REVERT: G 159 GLU cc_start: 0.7797 (mm-30) cc_final: 0.6988 (pm20) REVERT: G 160 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7127 (mtpt) REVERT: D 110 ARG cc_start: 0.7198 (mmm-85) cc_final: 0.6812 (mmm-85) REVERT: C 25 ASN cc_start: 0.7817 (t0) cc_final: 0.7405 (t160) REVERT: C 101 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: J 36 VAL cc_start: 0.4696 (t) cc_final: 0.4279 (p) outliers start: 53 outliers final: 20 residues processed: 312 average time/residue: 0.6023 time to fit residues: 215.7577 Evaluate side-chains 286 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN I 134 GLN C 38 ASN C 44 ASN C 75 ASN C 82 ASN J 282 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133139 restraints weight = 23528.370| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.96 r_work: 0.3345 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22816 Z= 0.185 Angle : 0.594 19.629 31023 Z= 0.325 Chirality : 0.044 0.392 3508 Planarity : 0.004 0.055 3755 Dihedral : 14.903 170.773 3832 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.25 % Favored : 93.72 % Rotamer: Outliers : 2.57 % Allowed : 13.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.50 (0.16), residues: 2594 helix: 1.00 (0.16), residues: 1111 sheet: -0.40 (0.26), residues: 368 loop : -1.71 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 91 TYR 0.017 0.002 TYR E 135 PHE 0.028 0.002 PHE E 26 TRP 0.009 0.002 TRP J 228 HIS 0.006 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (22811) covalent geometry : angle 0.58007 / 0.32 (31015) SS BOND : bond 0.01447 / 0.72 ( 4) SS BOND : angle 8.04566 / 4.51 ( 8) hydrogen bonds : bond 0.04298 / 2.87 ( 1013) hydrogen bonds : angle 5.22735 / 3.65 ( 2929) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: A 243 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7675 (t0) REVERT: A 249 MET cc_start: 0.8613 (tpp) cc_final: 0.8307 (tpp) REVERT: B 135 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8044 (t0) REVERT: B 200 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 273 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8564 (mm) REVERT: F 74 GLN cc_start: 0.7668 (tp40) cc_final: 0.7456 (tp40) REVERT: H 154 ASP cc_start: 0.7581 (t0) cc_final: 0.7315 (t0) REVERT: H 180 HIS cc_start: 0.9103 (OUTLIER) cc_final: 0.8631 (m170) REVERT: G 53 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.9026 (ttp) REVERT: G 159 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7037 (pm20) REVERT: D 110 ARG cc_start: 0.7139 (mmm-85) cc_final: 0.6814 (mmm-85) REVERT: C 25 ASN cc_start: 0.7682 (t0) cc_final: 0.7198 (t160) REVERT: C 101 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: J 81 MET cc_start: 0.4662 (mpp) cc_final: 0.4115 (mpm) outliers start: 58 outliers final: 28 residues processed: 301 average time/residue: 0.6188 time to fit residues: 213.6422 Evaluate side-chains 295 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 252 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 195 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 206 optimal weight: 0.0970 chunk 205 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN F 62 ASN E 73 ASN C 75 ASN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.176955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135757 restraints weight = 23823.004| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.97 r_work: 0.3386 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22816 Z= 0.124 Angle : 0.548 19.063 31023 Z= 0.302 Chirality : 0.042 0.383 3508 Planarity : 0.003 0.042 3755 Dihedral : 14.863 170.168 3832 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 2.04 % Allowed : 15.44 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.38 (0.16), residues: 2594 helix: 1.15 (0.16), residues: 1111 sheet: -0.43 (0.25), residues: 387 loop : -1.68 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 91 TYR 0.022 0.001 TYR A 458 PHE 0.030 0.001 PHE E 26 TRP 0.020 0.002 TRP J 228 HIS 0.006 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22811) covalent geometry : angle 0.53407 / 0.30 (31015) SS BOND : bond 0.01221 / 0.61 ( 4) SS BOND : angle 7.61941 / 4.30 ( 8) hydrogen bonds : bond 0.03823 / 2.54 ( 1013) hydrogen bonds : angle 5.05048 / 3.54 ( 2929) Misc. bond : bond 0.00095 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7065 (pp20) REVERT: A 171 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: A 243 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: A 249 MET cc_start: 0.8584 (tpp) cc_final: 0.8246 (tpp) REVERT: A 488 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.7828 (ttp-110) REVERT: B 135 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8028 (t0) REVERT: B 200 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 273 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8414 (mm) REVERT: F 204 LYS cc_start: 0.7914 (mttp) cc_final: 0.7421 (tppt) REVERT: H 154 ASP cc_start: 0.7554 (t0) cc_final: 0.7311 (t0) REVERT: H 180 HIS cc_start: 0.9011 (OUTLIER) cc_final: 0.8457 (m170) REVERT: G 151 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7348 (t0) REVERT: G 159 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7018 (pm20) REVERT: G 160 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7127 (mtpt) REVERT: I 122 THR cc_start: 0.5783 (OUTLIER) cc_final: 0.5562 (t) REVERT: E 73 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6846 (m110) REVERT: C 101 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: J 3 LYS cc_start: 0.7666 (mttm) cc_final: 0.7062 (mtpt) REVERT: J 36 VAL cc_start: 0.4530 (t) cc_final: 0.4072 (p) REVERT: J 162 GLU cc_start: 0.5522 (mm-30) cc_final: 0.5320 (mm-30) outliers start: 46 outliers final: 19 residues processed: 316 average time/residue: 0.5632 time to fit residues: 204.5412 Evaluate side-chains 304 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 216 optimal weight: 40.0000 chunk 158 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 680 ASN F 62 ASN E 73 ASN C 25 ASN C 75 ASN C 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135926 restraints weight = 23590.835| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.97 r_work: 0.3388 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22816 Z= 0.127 Angle : 0.549 18.958 31023 Z= 0.302 Chirality : 0.042 0.385 3508 Planarity : 0.003 0.051 3755 Dihedral : 14.828 170.222 3832 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 2.26 % Allowed : 16.28 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.34 (0.16), residues: 2594 helix: 1.19 (0.16), residues: 1112 sheet: -0.41 (0.25), residues: 393 loop : -1.68 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 369 TYR 0.014 0.001 TYR F 55 PHE 0.030 0.001 PHE E 26 TRP 0.016 0.001 TRP J 228 HIS 0.004 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (22811) covalent geometry : angle 0.53516 / 0.30 (31015) SS BOND : bond 0.01250 / 0.62 ( 4) SS BOND : angle 7.68929 / 4.32 ( 8) hydrogen bonds : bond 0.03792 / 2.52 ( 1013) hydrogen bonds : angle 4.99771 / 3.50 ( 2929) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7051 (pp20) REVERT: A 171 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: A 243 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: A 249 MET cc_start: 0.8556 (tpp) cc_final: 0.8226 (tpp) REVERT: A 488 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.7805 (ttp-110) REVERT: B 135 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8032 (t0) REVERT: B 200 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 260 LYS cc_start: 0.8492 (mttm) cc_final: 0.8278 (mtpp) REVERT: B 273 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8383 (mm) REVERT: F 204 LYS cc_start: 0.7895 (mttp) cc_final: 0.7432 (tppt) REVERT: H 154 ASP cc_start: 0.7553 (t0) cc_final: 0.7305 (t0) REVERT: H 180 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8423 (m170) REVERT: G 151 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7395 (t0) REVERT: G 159 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7104 (pm20) REVERT: G 160 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7128 (mtpt) REVERT: I 122 THR cc_start: 0.5872 (OUTLIER) cc_final: 0.5659 (t) REVERT: C 25 ASN cc_start: 0.7663 (t0) cc_final: 0.6996 (t0) REVERT: C 101 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: J 3 LYS cc_start: 0.7787 (mttm) cc_final: 0.7150 (mtpt) REVERT: J 36 VAL cc_start: 0.4495 (t) cc_final: 0.4056 (p) REVERT: J 162 GLU cc_start: 0.5742 (mm-30) cc_final: 0.5490 (mm-30) outliers start: 51 outliers final: 25 residues processed: 321 average time/residue: 0.5640 time to fit residues: 208.3689 Evaluate side-chains 301 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 101 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 241 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN F 62 ASN I 134 GLN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.176477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134828 restraints weight = 23558.241| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.95 r_work: 0.3374 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22816 Z= 0.147 Angle : 0.566 19.134 31023 Z= 0.310 Chirality : 0.043 0.388 3508 Planarity : 0.004 0.053 3755 Dihedral : 14.819 170.358 3832 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 2.17 % Allowed : 16.90 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.35 (0.16), residues: 2594 helix: 1.15 (0.16), residues: 1118 sheet: -0.39 (0.26), residues: 381 loop : -1.66 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 237 TYR 0.024 0.001 TYR A 458 PHE 0.031 0.002 PHE E 26 TRP 0.016 0.001 TRP J 228 HIS 0.005 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (22811) covalent geometry : angle 0.55165 / 0.30 (31015) SS BOND : bond 0.01318 / 0.66 ( 4) SS BOND : angle 7.80979 / 4.37 ( 8) hydrogen bonds : bond 0.03896 / 2.59 ( 1013) hydrogen bonds : angle 5.02127 / 3.52 ( 2929) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7026 (pp20) REVERT: A 171 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: A 243 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: A 249 MET cc_start: 0.8562 (tpp) cc_final: 0.8220 (tpp) REVERT: A 488 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.7857 (ttp-110) REVERT: B 18 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8368 (mtt90) REVERT: B 135 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8037 (t0) REVERT: B 200 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7387 (mt-10) REVERT: B 260 LYS cc_start: 0.8500 (mttm) cc_final: 0.8238 (mtpp) REVERT: B 273 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8414 (mm) REVERT: H 154 ASP cc_start: 0.7634 (t0) cc_final: 0.7376 (t0) REVERT: H 180 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8448 (m170) REVERT: G 151 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7365 (t0) REVERT: G 159 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7132 (pm20) REVERT: I 122 THR cc_start: 0.5838 (OUTLIER) cc_final: 0.5622 (t) REVERT: C 25 ASN cc_start: 0.7601 (t0) cc_final: 0.6899 (t0) REVERT: C 101 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7331 (pt0) REVERT: J 3 LYS cc_start: 0.7778 (mttm) cc_final: 0.7138 (mtpt) REVERT: J 36 VAL cc_start: 0.4465 (t) cc_final: 0.4029 (p) REVERT: J 162 GLU cc_start: 0.5699 (mm-30) cc_final: 0.5458 (mm-30) outliers start: 49 outliers final: 27 residues processed: 307 average time/residue: 0.5539 time to fit residues: 195.5560 Evaluate side-chains 297 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 241 optimal weight: 0.0040 chunk 126 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 254 optimal weight: 30.0000 chunk 247 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN A 646 GLN E 69 ASN C 75 ASN C 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132817 restraints weight = 23663.375| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.84 r_work: 0.3345 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22816 Z= 0.177 Angle : 0.591 19.427 31023 Z= 0.322 Chirality : 0.044 0.392 3508 Planarity : 0.004 0.045 3755 Dihedral : 14.842 170.516 3832 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.68 % Rotamer: Outliers : 2.17 % Allowed : 16.99 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.40 (0.16), residues: 2594 helix: 1.11 (0.16), residues: 1114 sheet: -0.40 (0.26), residues: 381 loop : -1.68 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 123 TYR 0.019 0.002 TYR E 135 PHE 0.032 0.002 PHE E 26 TRP 0.014 0.002 TRP J 228 HIS 0.006 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (22811) covalent geometry : angle 0.57702 / 0.32 (31015) SS BOND : bond 0.01439 / 0.72 ( 4) SS BOND : angle 8.01227 / 4.48 ( 8) hydrogen bonds : bond 0.04121 / 2.76 ( 1013) hydrogen bonds : angle 5.07735 / 3.55 ( 2929) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6996 (pp20) REVERT: A 171 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7099 (m-30) REVERT: A 249 MET cc_start: 0.8586 (tpp) cc_final: 0.8282 (tpp) REVERT: A 488 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.7808 (ttp-110) REVERT: B 18 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8345 (mtt90) REVERT: B 135 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8083 (t0) REVERT: B 200 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 260 LYS cc_start: 0.8523 (mttm) cc_final: 0.8262 (mtpp) REVERT: B 273 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8524 (mm) REVERT: F 1 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6589 (ptp) REVERT: H 154 ASP cc_start: 0.7614 (t0) cc_final: 0.7344 (t0) REVERT: H 180 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.8493 (m170) REVERT: G 151 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7313 (t0) REVERT: I 122 THR cc_start: 0.5785 (OUTLIER) cc_final: 0.5567 (t) REVERT: C 25 ASN cc_start: 0.7568 (t0) cc_final: 0.6844 (t0) REVERT: C 101 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: J 3 LYS cc_start: 0.7794 (mttm) cc_final: 0.7150 (mtpt) REVERT: J 36 VAL cc_start: 0.4452 (t) cc_final: 0.4020 (p) REVERT: J 81 MET cc_start: 0.4229 (mpp) cc_final: 0.3784 (mpm) REVERT: J 162 GLU cc_start: 0.5639 (mm-30) cc_final: 0.5322 (mm-30) outliers start: 49 outliers final: 26 residues processed: 302 average time/residue: 0.5388 time to fit residues: 187.1211 Evaluate side-chains 293 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 237 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN I 134 GLN C 38 ASN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.177971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137327 restraints weight = 23465.279| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.79 r_work: 0.3374 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 22816 Z= 0.140 Angle : 0.571 19.145 31023 Z= 0.313 Chirality : 0.043 0.387 3508 Planarity : 0.004 0.049 3755 Dihedral : 14.844 170.208 3832 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 1.59 % Allowed : 17.65 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.35 (0.16), residues: 2594 helix: 1.15 (0.16), residues: 1116 sheet: -0.39 (0.26), residues: 381 loop : -1.65 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 123 TYR 0.023 0.001 TYR A 458 PHE 0.032 0.001 PHE E 26 TRP 0.014 0.001 TRP J 228 HIS 0.005 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (22811) covalent geometry : angle 0.55745 / 0.31 (31015) SS BOND : bond 0.01298 / 0.65 ( 4) SS BOND : angle 7.77267 / 4.37 ( 8) hydrogen bonds : bond 0.03905 / 2.60 ( 1013) hydrogen bonds : angle 5.02028 / 3.52 ( 2929) Misc. bond : bond 0.00005 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7043 (pp20) REVERT: A 171 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: A 243 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: A 249 MET cc_start: 0.8577 (tpp) cc_final: 0.8290 (tpp) REVERT: A 488 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.7788 (ttp-110) REVERT: B 18 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8388 (mtt90) REVERT: B 135 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8050 (t0) REVERT: B 200 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 273 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8437 (mm) REVERT: H 180 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8433 (m170) REVERT: G 151 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7356 (t0) REVERT: G 159 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7104 (pm20) REVERT: I 122 THR cc_start: 0.5834 (OUTLIER) cc_final: 0.5610 (t) REVERT: C 25 ASN cc_start: 0.7616 (t0) cc_final: 0.6951 (t0) REVERT: C 75 ASN cc_start: 0.7558 (p0) cc_final: 0.7159 (t0) REVERT: J 3 LYS cc_start: 0.7773 (mttm) cc_final: 0.7101 (mtpt) REVERT: J 36 VAL cc_start: 0.4484 (t) cc_final: 0.4056 (p) REVERT: J 67 ASP cc_start: 0.4548 (m-30) cc_final: 0.4059 (m-30) outliers start: 36 outliers final: 25 residues processed: 289 average time/residue: 0.5432 time to fit residues: 180.3344 Evaluate side-chains 292 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 26 PHE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain J residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 261 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 94 optimal weight: 0.0040 chunk 14 optimal weight: 0.8980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN E 69 ASN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137593 restraints weight = 23513.126| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.88 r_work: 0.3370 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22816 Z= 0.143 Angle : 0.567 19.129 31023 Z= 0.311 Chirality : 0.043 0.387 3508 Planarity : 0.003 0.045 3755 Dihedral : 14.820 170.135 3832 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 2.08 % Allowed : 17.61 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % 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: -0.33 (0.16), residues: 2594 helix: 1.19 (0.16), residues: 1108 sheet: -0.39 (0.26), residues: 381 loop : -1.64 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.022 0.001 TYR E 135 PHE 0.032 0.001 PHE E 26 TRP 0.013 0.001 TRP J 228 HIS 0.005 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (22811) covalent geometry : angle 0.55350 / 0.31 (31015) SS BOND : bond 0.01296 / 0.65 ( 4) SS BOND : angle 7.77427 / 4.36 ( 8) hydrogen bonds : bond 0.03884 / 2.59 ( 1013) hydrogen bonds : angle 4.99281 / 3.50 ( 2929) Misc. bond : bond 0.00003 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8452.58 seconds wall clock time: 144 minutes 35.42 seconds (8675.42 seconds total)