Starting phenix.real_space_refine on Fri Sep 19 01:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ash_43814/09_2025/9ash_43814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ash_43814/09_2025/9ash_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_43814/09_2025/9ash_43814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ash_43814/09_2025/9ash_43814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ash_43814/09_2025/9ash_43814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ash_43814/09_2025/9ash_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 5.27, per 1000 atoms: 0.24 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: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.83 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: 4.49 Time building geometry restraints manager: 2.42 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=" CA CYS A 418 " pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " ideal model delta sigma weight residual 114.40 134.15 -19.75 2.30e+00 1.89e-01 7.37e+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: 3051 0.062 - 0.125: 418 0.125 - 0.187: 29 0.187 - 0.249: 5 0.249 - 0.311: 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 2.42e+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 2.45 2.16 0.29 2.00e-01 2.50e+01 2.09e+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: 3.120 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.200 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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= 0.363 Angle : 0.650 19.750 31023 Z= 0.393 Chirality : 0.043 0.311 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 aren 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 covalent geometry : bond 0.00518 (22811) covalent geometry : angle 0.63859 (31015) SS BOND : bond 0.01033 ( 4) SS BOND : angle 7.59364 ( 8) hydrogen bonds : bond 0.16126 ( 1013) hydrogen bonds : angle 7.13552 ( 2929) Misc. bond : bond 0.04155 ( 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 : 0.901 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: 0.6921 time to fit residues: 274.8980 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 : 0.933 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 H 201 ASN G 16 HIS I 72 ASN I 134 GLN I 206 ASN D 50 GLN E 22 ASN E 25 ASN E 65 ASN C 25 ASN C 39 HIS C 44 ASN C 73 ASN C 75 ASN C 82 ASN C 123 GLN J 38 HIS ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN J 301 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133370 restraints weight = 23397.086| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.95 r_work: 0.3318 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 22816 Z= 0.254 Angle : 0.689 20.754 31023 Z= 0.368 Chirality : 0.047 0.370 3508 Planarity : 0.004 0.044 3755 Dihedral : 15.067 169.848 3832 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.52 % Favored : 93.45 % Rotamer: Outliers : 2.04 % Allowed : 10.35 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.16), residues: 2594 helix: 0.75 (0.16), residues: 1112 sheet: -0.41 (0.26), residues: 368 loop : -1.71 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 21 TYR 0.022 0.002 TYR A 458 PHE 0.028 0.002 PHE E 26 TRP 0.008 0.002 TRP A 334 HIS 0.008 0.002 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00587 (22811) covalent geometry : angle 0.67578 (31015) SS BOND : bond 0.01557 ( 4) SS BOND : angle 8.32193 ( 8) hydrogen bonds : bond 0.04979 ( 1013) hydrogen bonds : angle 5.62690 ( 2929) Misc. bond : bond 0.00005 ( 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 327 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: A 243 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7690 (t0) REVERT: B 135 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 200 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7581 (mt-10) REVERT: F 59 LYS cc_start: 0.7967 (mttm) cc_final: 0.7596 (mtmt) REVERT: F 74 GLN cc_start: 0.7801 (tp40) cc_final: 0.7532 (tp-100) REVERT: F 116 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: H 180 HIS cc_start: 0.9111 (OUTLIER) cc_final: 0.8639 (m170) REVERT: G 90 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8327 (tpp80) REVERT: G 159 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7144 (pm20) REVERT: E 73 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.6948 (m110) REVERT: C 124 ARG cc_start: 0.7534 (mtt90) cc_final: 0.6779 (mtp-110) REVERT: J 36 VAL cc_start: 0.4736 (t) cc_final: 0.4301 (p) REVERT: J 51 GLU cc_start: 0.4783 (mm-30) cc_final: 0.3779 (tp30) REVERT: J 81 MET cc_start: 0.4835 (mpp) cc_final: 0.4281 (mpm) outliers start: 46 outliers final: 22 residues processed: 305 average time/residue: 0.6531 time to fit residues: 227.7081 Evaluate side-chains 287 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 243 ASP Chi-restraints excluded: chain A residue 257 VAL 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 F residue 116 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 H residue 206 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 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 73 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 261 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 244 optimal weight: 0.0370 chunk 16 optimal weight: 0.0070 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN A 646 GLN F 62 ASN H 180 HIS H 201 ASN I 134 GLN I 180 HIS E 73 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 = 0.4060 r_free = 0.4060 target = 0.177476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136623 restraints weight = 23794.341| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.98 r_work: 0.3396 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1455 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= 0.123 Angle : 0.558 19.184 31023 Z= 0.303 Chirality : 0.042 0.337 3508 Planarity : 0.003 0.043 3755 Dihedral : 14.886 169.125 3832 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 1.68 % Allowed : 12.88 % Favored : 85.44 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 2594 helix: 1.08 (0.16), residues: 1108 sheet: -0.42 (0.25), residues: 389 loop : -1.68 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.012 0.001 TYR F 55 PHE 0.023 0.001 PHE E 26 TRP 0.007 0.001 TRP A 334 HIS 0.013 0.001 HIS H 180 Details of bonding type rmsd covalent geometry : bond 0.00260 (22811) covalent geometry : angle 0.54463 (31015) SS BOND : bond 0.01149 ( 4) SS BOND : angle 7.54524 ( 8) hydrogen bonds : bond 0.03786 ( 1013) hydrogen bonds : angle 5.14297 ( 2929) Misc. bond : bond 0.00003 ( 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 336 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7021 (pp20) REVERT: A 243 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7581 (t0) REVERT: A 249 MET cc_start: 0.8435 (tpp) cc_final: 0.8142 (tpp) REVERT: A 488 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.7762 (ttp-110) REVERT: B 200 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7465 (mt-10) REVERT: F 59 LYS cc_start: 0.7936 (mttm) cc_final: 0.7595 (mtmt) REVERT: G 159 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7062 (pm20) REVERT: D 110 ARG cc_start: 0.7027 (mmm-85) cc_final: 0.6707 (mmm-85) REVERT: E 73 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6839 (m110) REVERT: C 25 ASN cc_start: 0.7694 (t0) cc_final: 0.7463 (t0) REVERT: C 124 ARG cc_start: 0.7524 (mtt90) cc_final: 0.6791 (mtp-110) REVERT: C 134 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7986 (mtm-85) REVERT: J 36 VAL cc_start: 0.4497 (t) cc_final: 0.4089 (p) REVERT: J 67 ASP cc_start: 0.4496 (m-30) cc_final: 0.4101 (m-30) outliers start: 38 outliers final: 11 residues processed: 319 average time/residue: 0.6539 time to fit residues: 238.4928 Evaluate side-chains 287 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 274 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 135 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 45 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 0.0060 chunk 184 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 61 optimal weight: 0.0570 chunk 244 optimal weight: 0.0270 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 680 ASN F 62 ASN H 180 HIS I 134 GLN E 73 ASN C 75 ASN C 82 ASN J 282 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140946 restraints weight = 23583.906| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.77 r_work: 0.3429 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 22816 Z= 0.110 Angle : 0.533 19.016 31023 Z= 0.289 Chirality : 0.041 0.317 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.755 168.912 3832 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 1.81 % Allowed : 14.78 % Favored : 83.41 % 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 aren not related in a simple way. whole: -0.24 (0.16), residues: 2594 helix: 1.26 (0.16), residues: 1110 sheet: -0.39 (0.25), residues: 396 loop : -1.59 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.021 0.001 TYR A 458 PHE 0.020 0.001 PHE E 26 TRP 0.007 0.001 TRP A 334 HIS 0.008 0.001 HIS H 180 Details of bonding type rmsd covalent geometry : bond 0.00229 (22811) covalent geometry : angle 0.51919 (31015) SS BOND : bond 0.01081 ( 4) SS BOND : angle 7.40302 ( 8) hydrogen bonds : bond 0.03477 ( 1013) hydrogen bonds : angle 4.91877 ( 2929) Misc. bond : bond 0.00011 ( 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 345 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7021 (pp20) REVERT: A 171 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: A 243 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7564 (t0) REVERT: A 249 MET cc_start: 0.8379 (tpp) cc_final: 0.8166 (tpp) REVERT: B 135 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8022 (t0) REVERT: B 200 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 266 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: F 1 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6687 (ptp) REVERT: F 116 GLU cc_start: 0.8545 (pt0) cc_final: 0.8245 (pt0) REVERT: F 204 LYS cc_start: 0.7887 (mttp) cc_final: 0.7459 (tppt) REVERT: H 116 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: G 159 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7077 (pm20) REVERT: E 73 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6972 (m110) REVERT: C 75 ASN cc_start: 0.7575 (p0) cc_final: 0.7146 (t0) REVERT: C 134 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7979 (mtm-85) REVERT: J 3 LYS cc_start: 0.7591 (mttm) cc_final: 0.7014 (mtpt) REVERT: J 36 VAL cc_start: 0.4633 (t) cc_final: 0.4215 (p) REVERT: J 67 ASP cc_start: 0.4515 (m-30) cc_final: 0.4256 (m-30) REVERT: J 162 GLU cc_start: 0.5705 (mm-30) cc_final: 0.5436 (mm-30) outliers start: 41 outliers final: 11 residues processed: 328 average time/residue: 0.6424 time to fit residues: 241.2735 Evaluate side-chains 291 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 243 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 109 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 131 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** H 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN I 134 GLN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.175354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134256 restraints weight = 23275.881| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.80 r_work: 0.3329 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 22816 Z= 0.220 Angle : 0.632 20.193 31023 Z= 0.338 Chirality : 0.045 0.378 3508 Planarity : 0.004 0.046 3755 Dihedral : 14.897 169.512 3832 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.48 % Rotamer: Outliers : 2.79 % Allowed : 15.66 % Favored : 81.55 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 2594 helix: 1.02 (0.16), residues: 1116 sheet: -0.32 (0.26), residues: 368 loop : -1.66 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.018 0.002 TYR B 186 PHE 0.025 0.002 PHE A 553 TRP 0.017 0.002 TRP J 228 HIS 0.011 0.001 HIS H 180 Details of bonding type rmsd covalent geometry : bond 0.00505 (22811) covalent geometry : angle 0.61819 (31015) SS BOND : bond 0.01516 ( 4) SS BOND : angle 8.12610 ( 8) hydrogen bonds : bond 0.04312 ( 1013) hydrogen bonds : angle 5.17338 ( 2929) Misc. bond : bond 0.00055 ( 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 334 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7074 (pp20) REVERT: A 171 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: A 243 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7674 (t0) REVERT: A 249 MET cc_start: 0.8513 (tpp) cc_final: 0.8280 (tpp) REVERT: A 488 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.7828 (ttp-110) REVERT: B 135 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8115 (t0) REVERT: B 200 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7470 (mt-10) REVERT: H 116 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: G 159 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7143 (pm20) REVERT: I 122 THR cc_start: 0.5944 (OUTLIER) cc_final: 0.5717 (t) REVERT: E 73 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7066 (m110) REVERT: C 101 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7308 (pt0) REVERT: J 3 LYS cc_start: 0.7671 (mttm) cc_final: 0.7082 (mtpt) REVERT: J 67 ASP cc_start: 0.4527 (m-30) cc_final: 0.4114 (m-30) outliers start: 63 outliers final: 20 residues processed: 316 average time/residue: 0.6069 time to fit residues: 220.0081 Evaluate side-chains 292 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain F residue 22 ASP 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 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE 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 Chi-restraints excluded: chain J residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 252 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 206 optimal weight: 20.0000 chunk 205 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 706 GLN H 180 HIS ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 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 = 0.4076 r_free = 0.4076 target = 0.178150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137644 restraints weight = 23605.512| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.79 r_work: 0.3378 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 22816 Z= 0.139 Angle : 0.567 19.396 31023 Z= 0.306 Chirality : 0.042 0.342 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.802 169.114 3832 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 2.26 % Allowed : 16.64 % Favored : 81.11 % 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 aren not related in a simple way. whole: -0.32 (0.16), residues: 2594 helix: 1.19 (0.16), residues: 1110 sheet: -0.36 (0.26), residues: 381 loop : -1.64 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 123 TYR 0.023 0.001 TYR A 458 PHE 0.024 0.001 PHE E 129 TRP 0.013 0.001 TRP J 228 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00305 (22811) covalent geometry : angle 0.55376 (31015) SS BOND : bond 0.01215 ( 4) SS BOND : angle 7.66160 ( 8) hydrogen bonds : bond 0.03745 ( 1013) hydrogen bonds : angle 4.97236 ( 2929) Misc. bond : bond 0.00009 ( 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 339 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7042 (pp20) REVERT: A 171 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: A 243 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7597 (t0) REVERT: A 249 MET cc_start: 0.8458 (tpp) cc_final: 0.8226 (tpp) REVERT: A 488 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.7778 (ttp-110) REVERT: B 135 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 200 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 266 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: B 273 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8390 (mm) REVERT: F 1 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6698 (ptp) REVERT: G 75 ASP cc_start: 0.8145 (t0) cc_final: 0.7330 (m-30) REVERT: G 159 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7123 (pm20) REVERT: I 122 THR cc_start: 0.5912 (OUTLIER) cc_final: 0.5699 (t) REVERT: E 73 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.6987 (m110) REVERT: C 75 ASN cc_start: 0.7545 (p0) cc_final: 0.7135 (t0) REVERT: C 101 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: J 3 LYS cc_start: 0.7627 (mttm) cc_final: 0.7043 (mtpt) REVERT: J 36 VAL cc_start: 0.4440 (t) cc_final: 0.4051 (p) REVERT: J 67 ASP cc_start: 0.4434 (m-30) cc_final: 0.4030 (m-30) REVERT: J 81 MET cc_start: 0.4298 (mpp) cc_final: 0.3786 (mpm) REVERT: J 162 GLU cc_start: 0.5722 (mm-30) cc_final: 0.5408 (mm-30) outliers start: 51 outliers final: 21 residues processed: 324 average time/residue: 0.6036 time to fit residues: 224.2527 Evaluate side-chains 310 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 309 HIS Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 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 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 152 LEU 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 E residue 125 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 121 optimal weight: 0.1980 chunk 90 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 216 optimal weight: 9.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 680 ASN ** G 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN E 69 ASN E 73 ASN C 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139734 restraints weight = 23454.802| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.76 r_work: 0.3401 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 22816 Z= 0.118 Angle : 0.545 19.019 31023 Z= 0.295 Chirality : 0.041 0.318 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.729 169.007 3832 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 2.08 % Allowed : 17.57 % Favored : 80.35 % 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 aren not related in a simple way. whole: -0.17 (0.17), residues: 2594 helix: 1.32 (0.16), residues: 1109 sheet: -0.29 (0.26), residues: 393 loop : -1.59 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 123 TYR 0.019 0.001 TYR E 135 PHE 0.020 0.001 PHE E 129 TRP 0.010 0.001 TRP J 228 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00252 (22811) covalent geometry : angle 0.53144 (31015) SS BOND : bond 0.01123 ( 4) SS BOND : angle 7.51337 ( 8) hydrogen bonds : bond 0.03506 ( 1013) hydrogen bonds : angle 4.83122 ( 2929) Misc. bond : bond 0.00008 ( 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 341 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7047 (pp20) REVERT: A 86 MET cc_start: 0.4944 (mtm) cc_final: 0.4117 (pmm) REVERT: A 171 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: A 243 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7569 (t0) REVERT: A 249 MET cc_start: 0.8402 (tpp) cc_final: 0.8123 (tpp) REVERT: A 488 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.7729 (ttp-110) REVERT: A 686 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5946 (mt-10) REVERT: B 135 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8094 (t0) REVERT: B 200 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 266 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: B 273 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8226 (mm) REVERT: F 1 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6648 (ptp) REVERT: F 116 GLU cc_start: 0.8479 (pt0) cc_final: 0.8151 (pt0) REVERT: F 204 LYS cc_start: 0.7925 (mttp) cc_final: 0.7489 (tppt) REVERT: G 75 ASP cc_start: 0.7953 (t0) cc_final: 0.7160 (m-30) REVERT: G 159 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7096 (pm20) REVERT: I 122 THR cc_start: 0.5985 (OUTLIER) cc_final: 0.5769 (t) REVERT: E 73 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.7063 (m110) REVERT: C 75 ASN cc_start: 0.7500 (p0) cc_final: 0.7134 (t0) REVERT: C 101 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: J 3 LYS cc_start: 0.7730 (mttm) cc_final: 0.7083 (mtpt) REVERT: J 36 VAL cc_start: 0.4561 (t) cc_final: 0.4177 (p) REVERT: J 67 ASP cc_start: 0.4726 (m-30) cc_final: 0.4217 (m-30) REVERT: J 162 GLU cc_start: 0.5755 (mm-30) cc_final: 0.5453 (mm-30) outliers start: 47 outliers final: 19 residues processed: 325 average time/residue: 0.5928 time to fit residues: 222.1121 Evaluate side-chains 300 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 266 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 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 152 LEU 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 Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU 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: 1.9990 chunk 241 optimal weight: 0.3980 chunk 182 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN A 646 GLN B 143 ASN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 ASN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN C 38 ASN C 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.176683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135895 restraints weight = 23349.279| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.79 r_work: 0.3344 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1773 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= 0.184 Angle : 0.606 19.571 31023 Z= 0.326 Chirality : 0.044 0.354 3508 Planarity : 0.004 0.045 3755 Dihedral : 14.820 169.452 3832 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 2.17 % Allowed : 17.88 % Favored : 79.96 % 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 aren not related in a simple way. whole: -0.32 (0.16), residues: 2594 helix: 1.17 (0.16), residues: 1108 sheet: -0.35 (0.26), residues: 376 loop : -1.61 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 123 TYR 0.023 0.002 TYR E 135 PHE 0.024 0.002 PHE E 129 TRP 0.009 0.002 TRP J 228 HIS 0.006 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00417 (22811) covalent geometry : angle 0.59286 (31015) SS BOND : bond 0.01430 ( 4) SS BOND : angle 7.96718 ( 8) hydrogen bonds : bond 0.04037 ( 1013) hydrogen bonds : angle 5.03673 ( 2929) Misc. bond : bond 0.00034 ( 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 317 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7054 (pp20) REVERT: A 86 MET cc_start: 0.5120 (mtm) cc_final: 0.4504 (pmm) REVERT: A 171 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: A 243 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7587 (t0) REVERT: A 249 MET cc_start: 0.8466 (tpp) cc_final: 0.8233 (tpp) REVERT: A 488 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.7865 (ttp-110) REVERT: A 686 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6228 (mt-10) REVERT: B 18 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8418 (mtt90) REVERT: B 135 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8120 (t0) REVERT: B 200 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7368 (mt-10) REVERT: B 266 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: B 273 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8466 (mm) REVERT: F 1 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6661 (ptp) REVERT: I 122 THR cc_start: 0.5878 (OUTLIER) cc_final: 0.5659 (t) REVERT: E 73 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7029 (m110) REVERT: C 75 ASN cc_start: 0.7519 (p0) cc_final: 0.7135 (t0) REVERT: C 101 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: J 3 LYS cc_start: 0.7719 (mttm) cc_final: 0.7097 (mtpt) REVERT: J 36 VAL cc_start: 0.4490 (t) cc_final: 0.4103 (p) REVERT: J 67 ASP cc_start: 0.4657 (m-30) cc_final: 0.4138 (m-30) REVERT: J 162 GLU cc_start: 0.5566 (mm-30) cc_final: 0.5277 (mm-30) outliers start: 49 outliers final: 25 residues processed: 307 average time/residue: 0.6203 time to fit residues: 218.8890 Evaluate side-chains 294 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 702 VAL 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 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 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 3 LEU 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 152 LEU 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 Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 241 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 254 optimal weight: 40.0000 chunk 247 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN A 646 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.173549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132608 restraints weight = 23239.947| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.87 r_work: 0.3296 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 22816 Z= 0.269 Angle : 0.692 20.269 31023 Z= 0.369 Chirality : 0.048 0.403 3508 Planarity : 0.004 0.050 3755 Dihedral : 14.975 170.160 3832 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.02 % Favored : 92.95 % Rotamer: Outliers : 2.52 % Allowed : 17.57 % Favored : 79.91 % 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 aren not related in a simple way. whole: -0.60 (0.16), residues: 2594 helix: 0.83 (0.16), residues: 1111 sheet: -0.29 (0.26), residues: 384 loop : -1.73 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 123 TYR 0.028 0.002 TYR E 135 PHE 0.027 0.002 PHE A 553 TRP 0.008 0.002 TRP J 228 HIS 0.009 0.002 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00623 (22811) covalent geometry : angle 0.67856 (31015) SS BOND : bond 0.01731 ( 4) SS BOND : angle 8.41963 ( 8) hydrogen bonds : bond 0.04648 ( 1013) hydrogen bonds : angle 5.34163 ( 2929) Misc. bond : bond 0.00072 ( 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 318 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.5411 (mtm) cc_final: 0.4930 (pmm) REVERT: A 171 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: A 243 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 18 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8500 (mtt90) REVERT: B 94 LYS cc_start: 0.7294 (mmtp) cc_final: 0.6726 (mtmt) REVERT: B 135 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8096 (t0) REVERT: B 200 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7431 (mt-10) REVERT: B 266 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: B 273 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8638 (mm) REVERT: F 1 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6351 (mtp) REVERT: G 75 ASP cc_start: 0.8014 (t0) cc_final: 0.7690 (t0) REVERT: G 159 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7131 (pm20) REVERT: I 122 THR cc_start: 0.5867 (OUTLIER) cc_final: 0.5653 (t) REVERT: D 86 ASP cc_start: 0.6458 (m-30) cc_final: 0.6257 (m-30) REVERT: E 73 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7054 (m110) REVERT: J 3 LYS cc_start: 0.7696 (mttm) cc_final: 0.7049 (mtpt) REVERT: J 67 ASP cc_start: 0.4567 (m-30) cc_final: 0.4133 (m-30) REVERT: J 81 MET cc_start: 0.4628 (mpp) cc_final: 0.4125 (mpm) REVERT: J 123 ARG cc_start: 0.6687 (tmm160) cc_final: 0.5587 (mtm110) REVERT: J 296 PHE cc_start: 0.2443 (m-10) cc_final: 0.2058 (t80) outliers start: 57 outliers final: 28 residues processed: 302 average time/residue: 0.6247 time to fit residues: 216.0801 Evaluate side-chains 293 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 702 VAL 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 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 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 3 LEU Chi-restraints excluded: chain H residue 129 VAL 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 I residue 117 VAL 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 E residue 125 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 237 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN C 38 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 = 0.4069 r_free = 0.4069 target = 0.177329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136872 restraints weight = 23349.031| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.86 r_work: 0.3358 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1839 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= 0.149 Angle : 0.595 19.223 31023 Z= 0.321 Chirality : 0.043 0.350 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.826 169.549 3832 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.25 % Favored : 93.72 % Rotamer: Outliers : 1.68 % Allowed : 18.76 % Favored : 79.56 % 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 aren not related in a simple way. whole: -0.37 (0.16), residues: 2594 helix: 1.13 (0.16), residues: 1106 sheet: -0.30 (0.25), residues: 391 loop : -1.69 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 123 TYR 0.027 0.001 TYR E 135 PHE 0.023 0.002 PHE E 42 TRP 0.011 0.001 TRP J 228 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00330 (22811) covalent geometry : angle 0.58168 (31015) SS BOND : bond 0.01258 ( 4) SS BOND : angle 7.79323 ( 8) hydrogen bonds : bond 0.03852 ( 1013) hydrogen bonds : angle 5.06613 ( 2929) Misc. bond : bond 0.00018 ( 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 308 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.5222 (mtm) cc_final: 0.4682 (pmm) REVERT: A 171 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: A 243 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7647 (t0) REVERT: A 430 ASP cc_start: 0.6940 (m-30) cc_final: 0.6592 (m-30) REVERT: A 456 LEU cc_start: 0.7566 (pp) cc_final: 0.7359 (pp) REVERT: B 18 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8397 (mtt90) REVERT: B 94 LYS cc_start: 0.7227 (mmtp) cc_final: 0.6690 (mtmt) REVERT: B 135 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 200 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 266 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: B 273 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8449 (mm) REVERT: F 1 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6633 (ptp) REVERT: G 159 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7006 (pm20) REVERT: I 122 THR cc_start: 0.5935 (OUTLIER) cc_final: 0.5722 (t) REVERT: E 73 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.6954 (m110) REVERT: C 75 ASN cc_start: 0.7467 (p0) cc_final: 0.7119 (t0) REVERT: J 3 LYS cc_start: 0.7717 (mttm) cc_final: 0.7056 (mtpt) REVERT: J 36 VAL cc_start: 0.4581 (t) cc_final: 0.4169 (p) REVERT: J 67 ASP cc_start: 0.4558 (m-30) cc_final: 0.4139 (m-30) REVERT: J 81 MET cc_start: 0.4362 (mpp) cc_final: 0.3861 (mpm) REVERT: J 296 PHE cc_start: 0.2334 (m-10) cc_final: 0.1929 (t80) outliers start: 38 outliers final: 20 residues processed: 298 average time/residue: 0.6064 time to fit residues: 207.8809 Evaluate side-chains 293 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 702 VAL 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 153 THR Chi-restraints excluded: chain B residue 266 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 G residue 100 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain I residue 117 VAL 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 E residue 125 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 347 ILE 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: 2.9990 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 73 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 = 0.4070 r_free = 0.4070 target = 0.177381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136807 restraints weight = 23341.126| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.86 r_work: 0.3358 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1857 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= 0.152 Angle : 0.595 19.288 31023 Z= 0.320 Chirality : 0.043 0.345 3508 Planarity : 0.004 0.045 3755 Dihedral : 14.791 169.558 3832 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.40 % Favored : 93.56 % Rotamer: Outliers : 1.77 % Allowed : 18.63 % Favored : 79.60 % 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 aren not related in a simple way. whole: -0.34 (0.16), residues: 2594 helix: 1.16 (0.16), residues: 1107 sheet: -0.35 (0.26), residues: 376 loop : -1.64 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 124 TYR 0.027 0.001 TYR E 135 PHE 0.021 0.002 PHE E 129 TRP 0.010 0.001 TRP J 228 HIS 0.004 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00339 (22811) covalent geometry : angle 0.58134 (31015) SS BOND : bond 0.01282 ( 4) SS BOND : angle 7.79605 ( 8) hydrogen bonds : bond 0.03853 ( 1013) hydrogen bonds : angle 5.03193 ( 2929) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9688.28 seconds wall clock time: 165 minutes 26.46 seconds (9926.46 seconds total)