Starting phenix.real_space_refine on Fri Jan 24 14:46:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ash_43814/01_2025/9ash_43814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ash_43814/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ash_43814/01_2025/9ash_43814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ash_43814/01_2025/9ash_43814.map" model { file = "/net/cci-nas-00/data/ceres_data/9ash_43814/01_2025/9ash_43814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ash_43814/01_2025/9ash_43814.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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, 'GLN:plan1': 1, 'ASP:plan': 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: 12.94, per 1000 atoms: 0.58 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: 6.09 Conformation dependent library (CDL) restraints added in 2.8 seconds 5188 Ramachandran restraints generated. 2594 Oldfield, 0 Emsley, 2594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4900 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 31 sheets defined 44.6% alpha, 14.8% beta 15 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 11.22 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: 9.17 Time building geometry restraints manager: 6.96 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: 2.950 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: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 59.750 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.050 ------------------------------------------------------------------------------- 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 22811 Z= 0.341 Angle : 0.639 19.750 31015 Z= 0.389 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 334 HIS 0.004 0.001 HIS A 363 PHE 0.018 0.001 PHE A 553 TYR 0.013 0.001 TYR B 186 ARG 0.007 0.000 ARG A 21 *********************** 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 : 2.436 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: 1.5554 time to fit residues: 618.1838 Evaluate side-chains 266 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 110 optimal weight: 0.0770 chunk 67 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 176 ASN A 251 ASN A 381 ASN 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 39 HIS C 73 ASN C 75 ASN C 82 ASN C 123 GLN J 38 HIS J 42 HIS J 65 HIS ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN J 301 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133048 restraints weight = 23746.210| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.84 r_work: 0.3342 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 22811 Z= 0.277 Angle : 0.617 20.144 31015 Z= 0.333 Chirality : 0.045 0.344 3508 Planarity : 0.004 0.040 3755 Dihedral : 14.983 169.460 3832 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 1.59 % Allowed : 10.22 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2594 helix: 0.90 (0.16), residues: 1110 sheet: -0.43 (0.26), residues: 389 loop : -1.70 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 334 HIS 0.006 0.001 HIS A 363 PHE 0.028 0.002 PHE E 26 TYR 0.023 0.002 TYR A 458 ARG 0.008 0.001 ARG A 21 *********************** 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 324 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 2.608 Fit side-chains revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: A 243 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7599 (t0) REVERT: A 249 MET cc_start: 0.8620 (tpp) cc_final: 0.8291 (tpp) REVERT: A 488 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.7696 (ttp-110) REVERT: B 200 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7438 (mt-10) REVERT: F 74 GLN cc_start: 0.7720 (tp40) cc_final: 0.7440 (tp-100) REVERT: H 154 ASP cc_start: 0.7645 (t0) cc_final: 0.7413 (t0) REVERT: H 180 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8526 (m170) REVERT: G 159 GLU cc_start: 0.7808 (mm-30) cc_final: 0.6886 (pm20) REVERT: G 160 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.6971 (mtpt) REVERT: I 174 PHE cc_start: 0.7617 (m-80) cc_final: 0.6911 (m-80) REVERT: E 73 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6783 (m110) REVERT: E 137 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 124 ARG cc_start: 0.7477 (mtt90) cc_final: 0.6707 (mtp-110) REVERT: J 36 VAL cc_start: 0.4411 (t) cc_final: 0.4009 (p) REVERT: J 51 GLU cc_start: 0.4782 (mm-30) cc_final: 0.3721 (mm-30) outliers start: 36 outliers final: 17 residues processed: 308 average time/residue: 1.4721 time to fit residues: 517.0868 Evaluate side-chains 280 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 2.669 ------------------------------------------------------------------------------- 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 535 ASP Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 138 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS F 62 ASN H 180 HIS G 111 ASN I 134 GLN C 44 ASN C 75 ASN C 82 ASN ** J 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132084 restraints weight = 23592.445| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.90 r_work: 0.3333 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 22811 Z= 0.294 Angle : 0.611 20.076 31015 Z= 0.330 Chirality : 0.045 0.356 3508 Planarity : 0.004 0.049 3755 Dihedral : 14.936 169.790 3832 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 2.35 % Allowed : 12.17 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2594 helix: 0.89 (0.16), residues: 1111 sheet: -0.37 (0.26), residues: 368 loop : -1.71 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 334 HIS 0.010 0.001 HIS H 180 PHE 0.023 0.002 PHE A 553 TYR 0.015 0.002 TYR B 186 ARG 0.008 0.000 ARG A 21 *********************** 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 331 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 2.463 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: A 171 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: A 243 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7653 (t0) REVERT: A 249 MET cc_start: 0.8601 (tpp) cc_final: 0.8338 (tpp) REVERT: B 135 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8057 (t0) REVERT: B 200 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7466 (mt-10) REVERT: F 74 GLN cc_start: 0.7666 (tp40) cc_final: 0.7380 (tp40) REVERT: F 116 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: G 111 ASN cc_start: 0.8465 (t0) cc_final: 0.8263 (t0) REVERT: G 159 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7067 (pm20) REVERT: E 73 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.6846 (m110) REVERT: C 124 ARG cc_start: 0.7501 (mtt90) cc_final: 0.6770 (mtp-110) outliers start: 53 outliers final: 23 residues processed: 308 average time/residue: 1.4347 time to fit residues: 504.7628 Evaluate side-chains 290 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP 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 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 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 G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS A 180 GLN A 646 GLN F 62 ASN H 180 HIS G 151 ASN I 134 GLN I 180 HIS E 73 ASN C 25 ASN C 75 ASN C 82 ASN J 282 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136441 restraints weight = 23653.984| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.84 r_work: 0.3367 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 22811 Z= 0.198 Angle : 0.557 19.436 31015 Z= 0.302 Chirality : 0.042 0.344 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.851 169.258 3832 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 2.21 % Allowed : 14.73 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2594 helix: 1.08 (0.16), residues: 1110 sheet: -0.42 (0.26), residues: 375 loop : -1.67 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.007 0.001 HIS H 180 PHE 0.018 0.001 PHE E 129 TYR 0.023 0.001 TYR A 458 ARG 0.005 0.000 ARG D 110 *********************** 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 331 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 281 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7032 (pp20) REVERT: A 171 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: A 243 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7577 (t0) REVERT: A 249 MET cc_start: 0.8582 (tpp) cc_final: 0.8261 (tpp) REVERT: A 488 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.7829 (ttp-110) REVERT: B 135 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8046 (t0) REVERT: B 200 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7463 (mt-10) REVERT: F 1 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6633 (ptp) REVERT: F 74 GLN cc_start: 0.7729 (tp40) cc_final: 0.7473 (tp40) REVERT: G 111 ASN cc_start: 0.8504 (t0) cc_final: 0.8216 (t0) REVERT: G 151 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7425 (t0) REVERT: G 159 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7069 (pm20) REVERT: D 110 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6700 (mmm-85) REVERT: E 73 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.6858 (m110) REVERT: C 101 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: C 124 ARG cc_start: 0.7466 (mtt90) cc_final: 0.6725 (mtp-110) REVERT: J 3 LYS cc_start: 0.7639 (mttm) cc_final: 0.7036 (mtpt) REVERT: J 36 VAL cc_start: 0.4500 (t) cc_final: 0.4060 (p) REVERT: J 67 ASP cc_start: 0.4499 (m-30) cc_final: 0.4089 (m-30) outliers start: 50 outliers final: 16 residues processed: 311 average time/residue: 1.3966 time to fit residues: 495.6044 Evaluate side-chains 293 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain C residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 223 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 174 HIS A 646 GLN A 680 ASN H 180 HIS I 134 GLN C 38 ASN C 75 ASN C 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.176283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135244 restraints weight = 23690.700| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.94 r_work: 0.3367 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 22811 Z= 0.196 Angle : 0.551 19.417 31015 Z= 0.299 Chirality : 0.042 0.340 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.818 169.202 3832 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.68 % Rotamer: Outliers : 2.61 % Allowed : 15.44 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2594 helix: 1.15 (0.16), residues: 1112 sheet: -0.38 (0.26), residues: 375 loop : -1.65 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.004 0.001 HIS H 180 PHE 0.022 0.001 PHE E 129 TYR 0.015 0.001 TYR E 135 ARG 0.005 0.000 ARG D 110 *********************** 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 339 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 280 time to evaluate : 2.451 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7038 (pp20) REVERT: A 171 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: A 243 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7599 (t0) REVERT: A 249 MET cc_start: 0.8570 (tpp) cc_final: 0.8273 (tpp) REVERT: A 488 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.7839 (ttp-110) REVERT: B 135 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8049 (t0) REVERT: B 200 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7453 (mt-10) REVERT: B 266 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: B 273 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8453 (mm) REVERT: F 1 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6601 (ptp) REVERT: H 116 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: G 88 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7831 (pttt) REVERT: G 111 ASN cc_start: 0.8569 (t0) cc_final: 0.8310 (t0) REVERT: G 159 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7116 (pm20) REVERT: I 122 THR cc_start: 0.5850 (OUTLIER) cc_final: 0.5627 (t) REVERT: D 110 ARG cc_start: 0.7044 (mmm-85) cc_final: 0.6775 (mmm-85) REVERT: E 73 ASN cc_start: 0.7355 (m110) cc_final: 0.6906 (m110) REVERT: C 25 ASN cc_start: 0.7883 (t160) cc_final: 0.7457 (t160) REVERT: C 101 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: J 3 LYS cc_start: 0.7780 (mttm) cc_final: 0.7120 (mtpt) REVERT: J 36 VAL cc_start: 0.4559 (t) cc_final: 0.4128 (p) REVERT: J 67 ASP cc_start: 0.4499 (m-30) cc_final: 0.4089 (m-30) outliers start: 59 outliers final: 24 residues processed: 324 average time/residue: 1.3939 time to fit residues: 518.0143 Evaluate side-chains 300 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 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 H residue 101 LEU Chi-restraints excluded: chain H residue 116 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 177 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 125 THR 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 163 optimal weight: 0.0050 chunk 176 optimal weight: 8.9990 chunk 221 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 243 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 136 optimal weight: 0.0770 chunk 209 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 overall best weight: 0.6754 ------------------------------------------------------------------------------- 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 174 HIS A 646 GLN H 180 HIS I 134 GLN C 25 ASN C 38 ASN C 75 ASN C 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.178599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138017 restraints weight = 23531.833| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.86 r_work: 0.3393 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22811 Z= 0.176 Angle : 0.539 19.138 31015 Z= 0.293 Chirality : 0.042 0.334 3508 Planarity : 0.003 0.044 3755 Dihedral : 14.779 169.015 3832 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 2.39 % Allowed : 16.19 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2594 helix: 1.26 (0.16), residues: 1107 sheet: -0.35 (0.26), residues: 393 loop : -1.63 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.008 0.001 HIS H 180 PHE 0.020 0.001 PHE E 129 TYR 0.022 0.001 TYR A 458 ARG 0.005 0.000 ARG J 123 *********************** 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 338 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 2.803 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7021 (pp20) REVERT: A 171 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: A 243 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7613 (t0) REVERT: A 249 MET cc_start: 0.8542 (tpp) cc_final: 0.8247 (tpp) REVERT: A 488 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.7791 (ttp-110) REVERT: B 135 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8066 (t0) REVERT: B 200 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 266 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: B 273 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8380 (mm) REVERT: F 1 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6594 (ptp) REVERT: H 116 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: G 88 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7845 (pttt) REVERT: G 111 ASN cc_start: 0.8564 (t0) cc_final: 0.8277 (t0) REVERT: G 151 ASN cc_start: 0.7900 (p0) cc_final: 0.7440 (t0) REVERT: G 159 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7058 (pm20) REVERT: I 122 THR cc_start: 0.5836 (OUTLIER) cc_final: 0.5626 (t) REVERT: E 73 ASN cc_start: 0.7506 (m110) cc_final: 0.6996 (m110) REVERT: C 25 ASN cc_start: 0.7684 (t0) cc_final: 0.6999 (t0) REVERT: C 75 ASN cc_start: 0.7572 (p0) cc_final: 0.7138 (t0) REVERT: J 3 LYS cc_start: 0.7786 (mttm) cc_final: 0.7149 (mtpt) REVERT: J 36 VAL cc_start: 0.4372 (t) cc_final: 0.4016 (p) REVERT: J 67 ASP cc_start: 0.4491 (m-30) cc_final: 0.4101 (m-30) REVERT: J 81 MET cc_start: 0.4294 (mpp) cc_final: 0.3781 (mpm) outliers start: 54 outliers final: 24 residues processed: 322 average time/residue: 1.3734 time to fit residues: 507.0403 Evaluate side-chains 308 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 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 H residue 116 GLU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 177 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 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 52 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 174 HIS A 646 GLN A 680 ASN H 180 HIS I 134 GLN E 69 ASN E 73 ASN C 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.178377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137917 restraints weight = 23539.623| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.85 r_work: 0.3374 rms_B_bonded: 2.46 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: 0.7982 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 22811 Z= 0.198 Angle : 0.550 19.217 31015 Z= 0.298 Chirality : 0.042 0.334 3508 Planarity : 0.003 0.043 3755 Dihedral : 14.769 169.132 3832 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 2.83 % Allowed : 16.68 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2594 helix: 1.26 (0.16), residues: 1107 sheet: -0.35 (0.26), residues: 381 loop : -1.60 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 228 HIS 0.008 0.001 HIS H 180 PHE 0.021 0.001 PHE E 129 TYR 0.013 0.001 TYR I 55 ARG 0.005 0.000 ARG J 123 *********************** 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 347 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7073 (pp20) REVERT: A 86 MET cc_start: 0.5260 (mtm) cc_final: 0.4802 (ptt) REVERT: A 171 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: A 243 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7612 (t0) REVERT: A 249 MET cc_start: 0.8528 (tpp) cc_final: 0.8253 (tpp) REVERT: A 488 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.7830 (ttp-110) REVERT: B 135 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8101 (t0) REVERT: B 200 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 266 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: B 273 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8388 (mm) REVERT: F 1 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6625 (ptp) REVERT: G 88 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7861 (pttt) REVERT: G 111 ASN cc_start: 0.8592 (t0) cc_final: 0.8321 (t0) REVERT: G 151 ASN cc_start: 0.7865 (p0) cc_final: 0.7496 (t0) REVERT: G 159 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7127 (pm20) REVERT: I 122 THR cc_start: 0.5876 (OUTLIER) cc_final: 0.5651 (t) REVERT: E 73 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7076 (m110) REVERT: C 25 ASN cc_start: 0.7582 (t0) cc_final: 0.6971 (t0) REVERT: C 75 ASN cc_start: 0.7550 (p0) cc_final: 0.7149 (t0) REVERT: J 3 LYS cc_start: 0.7781 (mttm) cc_final: 0.7115 (mtpt) REVERT: J 36 VAL cc_start: 0.4557 (t) cc_final: 0.4132 (p) REVERT: J 67 ASP cc_start: 0.4536 (m-30) cc_final: 0.4135 (m-30) outliers start: 64 outliers final: 27 residues processed: 329 average time/residue: 1.3827 time to fit residues: 523.0855 Evaluate side-chains 305 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.768 ------------------------------------------------------------------------------- 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 309 HIS Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 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 H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 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 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 76 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 174 HIS A 646 GLN H 180 HIS 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 = 0.4072 r_free = 0.4072 target = 0.177741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137112 restraints weight = 23491.829| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.83 r_work: 0.3362 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22811 Z= 0.227 Angle : 0.567 19.317 31015 Z= 0.307 Chirality : 0.043 0.340 3508 Planarity : 0.003 0.043 3755 Dihedral : 14.790 169.260 3832 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 2.17 % Allowed : 17.43 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2594 helix: 1.22 (0.16), residues: 1108 sheet: -0.36 (0.26), residues: 381 loop : -1.63 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 228 HIS 0.006 0.001 HIS H 180 PHE 0.021 0.002 PHE E 129 TYR 0.024 0.001 TYR A 458 ARG 0.007 0.000 ARG B 18 *********************** 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 322 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 2.621 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7075 (pp20) REVERT: A 86 MET cc_start: 0.5238 (mtm) cc_final: 0.4756 (ptt) REVERT: A 171 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: A 243 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7629 (t0) REVERT: A 249 MET cc_start: 0.8540 (tpp) cc_final: 0.8260 (tpp) REVERT: A 488 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.7821 (ttp-110) REVERT: B 135 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8102 (t0) REVERT: B 200 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7361 (mt-10) REVERT: B 266 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: B 273 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8427 (mm) REVERT: H 180 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8630 (m170) REVERT: G 88 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7869 (pttt) REVERT: G 111 ASN cc_start: 0.8602 (t0) cc_final: 0.8313 (t0) REVERT: G 151 ASN cc_start: 0.7939 (p0) cc_final: 0.7479 (t0) REVERT: I 122 THR cc_start: 0.5848 (OUTLIER) cc_final: 0.5630 (t) REVERT: C 25 ASN cc_start: 0.7628 (t0) cc_final: 0.7077 (t0) REVERT: C 75 ASN cc_start: 0.7540 (p0) cc_final: 0.7141 (t0) REVERT: J 3 LYS cc_start: 0.7803 (mttm) cc_final: 0.7134 (mtpt) REVERT: J 36 VAL cc_start: 0.4523 (t) cc_final: 0.4104 (p) REVERT: J 67 ASP cc_start: 0.4480 (m-30) cc_final: 0.4083 (m-30) REVERT: J 81 MET cc_start: 0.4346 (mpp) cc_final: 0.3857 (mpm) outliers start: 49 outliers final: 27 residues processed: 308 average time/residue: 1.3529 time to fit residues: 477.2872 Evaluate side-chains 301 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 177 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 125 THR Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 169 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 9 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- 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 174 HIS A 646 GLN H 180 HIS C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.179333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138953 restraints weight = 23512.259| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.80 r_work: 0.3390 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22811 Z= 0.180 Angle : 0.545 18.968 31015 Z= 0.296 Chirality : 0.042 0.334 3508 Planarity : 0.003 0.043 3755 Dihedral : 14.755 169.153 3832 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.06 % Rotamer: Outliers : 2.30 % Allowed : 17.39 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2594 helix: 1.28 (0.16), residues: 1109 sheet: -0.32 (0.26), residues: 393 loop : -1.63 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 228 HIS 0.010 0.001 HIS H 180 PHE 0.021 0.001 PHE E 129 TYR 0.019 0.001 TYR E 135 ARG 0.005 0.000 ARG J 123 *********************** 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 332 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7053 (pp20) REVERT: A 86 MET cc_start: 0.5046 (mtm) cc_final: 0.4452 (pmm) REVERT: A 171 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: A 243 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7601 (t0) REVERT: A 249 MET cc_start: 0.8505 (tpp) cc_final: 0.8196 (tpp) REVERT: B 135 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 200 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 266 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: B 273 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8299 (mm) REVERT: F 1 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6670 (ptp) REVERT: G 88 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7881 (pttt) REVERT: G 111 ASN cc_start: 0.8610 (t0) cc_final: 0.8320 (t0) REVERT: G 151 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7497 (t0) REVERT: G 159 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7040 (pm20) REVERT: I 122 THR cc_start: 0.5832 (OUTLIER) cc_final: 0.5619 (t) REVERT: E 73 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7183 (m110) REVERT: C 25 ASN cc_start: 0.7648 (t0) cc_final: 0.7207 (t0) REVERT: C 75 ASN cc_start: 0.7532 (p0) cc_final: 0.7140 (t0) REVERT: J 3 LYS cc_start: 0.7732 (mttm) cc_final: 0.7080 (mtpt) REVERT: J 36 VAL cc_start: 0.4412 (t) cc_final: 0.4056 (p) REVERT: J 67 ASP cc_start: 0.4509 (m-30) cc_final: 0.4115 (m-30) REVERT: J 81 MET cc_start: 0.4138 (mpp) cc_final: 0.3641 (mpm) outliers start: 52 outliers final: 31 residues processed: 317 average time/residue: 1.3732 time to fit residues: 502.3461 Evaluate side-chains 314 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 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 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 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 340 LEU 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 104 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 72 optimal weight: 0.0770 chunk 217 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 680 ASN ** H 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133773 restraints weight = 23532.293| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.92 r_work: 0.3304 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 22811 Z= 0.364 Angle : 0.651 19.973 31015 Z= 0.349 Chirality : 0.047 0.386 3508 Planarity : 0.004 0.045 3755 Dihedral : 14.914 169.760 3832 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.98 % Favored : 92.98 % Rotamer: Outliers : 2.12 % Allowed : 17.65 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2594 helix: 0.97 (0.16), residues: 1113 sheet: -0.44 (0.25), residues: 401 loop : -1.68 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 228 HIS 0.013 0.002 HIS H 180 PHE 0.025 0.002 PHE A 553 TYR 0.026 0.002 TYR E 135 ARG 0.007 0.001 ARG J 123 ********************** 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 320 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 2.530 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7061 (pp20) REVERT: A 86 MET cc_start: 0.5323 (mtm) cc_final: 0.4698 (pmm) REVERT: A 171 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7057 (m-30) REVERT: A 243 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7682 (t0) REVERT: A 249 MET cc_start: 0.8561 (tpp) cc_final: 0.8295 (tpp) REVERT: B 94 LYS cc_start: 0.7251 (mmtp) cc_final: 0.6679 (mtmt) REVERT: B 135 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8130 (t0) REVERT: B 200 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7464 (mt-10) REVERT: B 273 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8606 (mm) REVERT: F 1 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6680 (ptp) REVERT: G 53 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8844 (ttp) REVERT: G 88 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7840 (pttt) REVERT: G 111 ASN cc_start: 0.8573 (t0) cc_final: 0.8268 (t0) REVERT: G 159 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7189 (pm20) REVERT: I 122 THR cc_start: 0.5816 (OUTLIER) cc_final: 0.5594 (t) REVERT: D 86 ASP cc_start: 0.6557 (m-30) cc_final: 0.6345 (m-30) REVERT: E 73 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7062 (m110) REVERT: C 25 ASN cc_start: 0.7553 (t0) cc_final: 0.7106 (t0) REVERT: J 3 LYS cc_start: 0.7794 (mttm) cc_final: 0.7181 (mtpt) REVERT: J 67 ASP cc_start: 0.4588 (m-30) cc_final: 0.4177 (m-30) outliers start: 48 outliers final: 31 residues processed: 309 average time/residue: 1.3323 time to fit residues: 471.5994 Evaluate side-chains 305 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain F residue 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 101 LEU Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain I residue 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 137 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 109 optimal weight: 2.9990 chunk 243 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 174 HIS A 460 GLN H 180 HIS ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.177421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136418 restraints weight = 23704.426| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.93 r_work: 0.3387 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 22811 Z= 0.173 Angle : 0.551 18.893 31015 Z= 0.299 Chirality : 0.042 0.332 3508 Planarity : 0.003 0.043 3755 Dihedral : 14.774 169.300 3832 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 1.77 % Allowed : 18.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2594 helix: 1.24 (0.16), residues: 1107 sheet: -0.40 (0.26), residues: 390 loop : -1.60 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 228 HIS 0.004 0.001 HIS A 363 PHE 0.023 0.001 PHE E 26 TYR 0.023 0.001 TYR E 135 ARG 0.004 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19416.33 seconds wall clock time: 345 minutes 24.66 seconds (20724.66 seconds total)