Starting phenix.real_space_refine on Sun Jun 15 17:24:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xn5_22268/06_2025/6xn5_22268.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xn5_22268/06_2025/6xn5_22268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xn5_22268/06_2025/6xn5_22268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xn5_22268/06_2025/6xn5_22268.map" model { file = "/net/cci-nas-00/data/ceres_data/6xn5_22268/06_2025/6xn5_22268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xn5_22268/06_2025/6xn5_22268.cif" } resolution = 2.97 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= 0.013 sd= 1.147 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 47 5.16 5 C 10948 2.51 5 N 2946 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17400 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 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: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 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: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1629 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 5939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5939 Classifications: {'peptide': 735} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 723} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2278 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2323 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 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: "J" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1917 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 227} Chain breaks: 3 Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 674 Classifications: {'RNA': 32} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 17, 'rna3p': 14} Time building chain proxies: 9.79, per 1000 atoms: 0.56 Number of scatterers: 17400 At special positions: 0 Unit cell: (122.436, 126.732, 205.134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 31 15.00 O 3428 8.00 N 2946 7.00 C 10948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.00 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=2.07 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.06 Conformation dependent library (CDL) restraints added in 2.3 seconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 27 sheets defined 37.5% alpha, 16.4% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 6.23 Creating SS restraints... Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 74 through 81 Processing helix chain 'I' and resid 103 through 109 removed outlier: 3.700A pdb=" N LEU I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 173 Processing helix chain 'I' and resid 204 through 213 removed outlier: 4.285A pdb=" N LEU I 208 " --> pdb=" O LYS I 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 74 through 82 Processing helix chain 'F' and resid 103 through 110 removed outlier: 3.910A pdb=" N PHE F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 205 through 213 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.614A pdb=" N PHE H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 157 through 173 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 72 through 85 removed outlier: 3.596A pdb=" N THR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.636A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (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 202 through 224 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.953A pdb=" N GLU A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 268 through 271 removed outlier: 3.531A pdb=" N LYS A 271 " --> pdb=" O LYS A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 271' Processing helix chain 'A' and resid 272 through 295 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 358 Processing helix chain 'A' and resid 363 through 381 removed outlier: 4.178A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.581A pdb=" N ASP A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 463 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.720A pdb=" N VAL A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.745A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.298A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 638 removed outlier: 3.518A pdb=" N TYR A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 Processing helix chain 'A' and resid 686 through 704 removed outlier: 3.919A pdb=" N ALA A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 725 removed outlier: 3.678A pdb=" N ILE A 710 " --> pdb=" O GLN A 706 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE A 724 " --> pdb=" O MET A 720 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.537A pdb=" N ASN B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.770A pdb=" N TYR B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.681A pdb=" N ALA B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'G' and resid 45 through 61 removed outlier: 3.501A pdb=" N LEU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 154 through 174 removed outlier: 3.527A pdb=" N VAL G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS G 160 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 212 Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.124A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 227 removed outlier: 3.897A pdb=" N ASN J 215 " --> pdb=" O LYS J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 235 removed outlier: 3.570A pdb=" N GLY J 232 " --> pdb=" O TRP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 300 Processing sheet with id=AA1, first strand: chain 'I' and resid 188 through 191 removed outlier: 3.750A pdb=" N ILE I 196 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 188 through 191 removed outlier: 6.271A pdb=" N GLU I 147 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN I 97 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY H 184 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE I 96 " --> pdb=" O GLY H 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'I' and resid 115 through 119 Processing sheet with id=AA5, first strand: chain 'F' and resid 188 through 199 removed outlier: 5.286A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU F 147 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN F 97 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY B 185 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE F 96 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'F' and resid 83 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.119A pdb=" N ASN G 97 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU G 147 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR G 8 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN G 192 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 10 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE G 190 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 143 through 151 removed outlier: 4.718A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB3, first strand: chain 'H' and resid 96 through 97 removed outlier: 6.715A pdb=" N PHE H 96 " --> pdb=" O GLY G 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 120 Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.497A pdb=" N LEU A 107 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.730A pdb=" N TYR A 311 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 305 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 344 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 302 through 305 removed outlier: 6.730A pdb=" N TYR A 311 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 305 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 350 " --> pdb=" O MET A 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.700A pdb=" N LYS A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 568 through 572 removed outlier: 6.482A pdb=" N PHE A 579 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 653 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC2, first strand: chain 'B' and resid 123 through 132 Processing sheet with id=AC3, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AC4, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.505A pdb=" N LEU B 256 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.592A pdb=" N ASP B 272 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 284 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AC8, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.073A pdb=" N VAL J 158 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER J 202 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP J 160 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR J 200 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE J 203 " --> pdb=" O LYS J 3 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR J 8 " --> pdb=" O LYS J 348 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS J 348 " --> pdb=" O THR J 8 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR J 10 " --> pdb=" O ARG J 346 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG J 346 " --> pdb=" O THR J 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA J 345 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE J 268 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 169 through 172 removed outlier: 3.932A pdb=" N LYS J 170 " --> pdb=" O CYS J 190 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS J 190 " --> pdb=" O LYS J 170 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR J 172 " --> pdb=" O ARG J 188 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG J 188 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 690 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5533 1.34 - 1.46: 4258 1.46 - 1.59: 7833 1.59 - 1.72: 42 1.72 - 1.84: 87 Bond restraints: 17753 Sorted by residual: bond pdb=" CA GLU A 704 " pdb=" C GLU A 704 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.80e-02 3.09e+03 8.24e+00 bond pdb=" CB PRO I 70 " pdb=" CG PRO I 70 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.93e+00 bond pdb=" N PRO I 70 " pdb=" CD PRO I 70 " ideal model delta sigma weight residual 1.473 1.504 -0.031 1.40e-02 5.10e+03 4.80e+00 bond pdb=" CG1 ILE G 139 " pdb=" CD1 ILE G 139 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.62e+00 bond pdb=" N ASP J 112 " pdb=" CA ASP J 112 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.93e+00 ... (remaining 17748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 23476 3.16 - 6.32: 486 6.32 - 9.48: 65 9.48 - 12.64: 10 12.64 - 15.80: 3 Bond angle restraints: 24040 Sorted by residual: angle pdb=" CA PRO I 70 " pdb=" N PRO I 70 " pdb=" CD PRO I 70 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.24e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 113.71 106.06 7.65 9.50e-01 1.11e+00 6.49e+01 angle pdb=" C LYS A 683 " pdb=" N LEU A 684 " pdb=" CA LEU A 684 " ideal model delta sigma weight residual 121.70 133.14 -11.44 1.80e+00 3.09e-01 4.04e+01 angle pdb=" N VAL J 277 " pdb=" CA VAL J 277 " pdb=" C VAL J 277 " ideal model delta sigma weight residual 112.96 107.06 5.90 1.00e+00 1.00e+00 3.48e+01 angle pdb=" CA CYS A 405 " pdb=" CB CYS A 405 " pdb=" SG CYS A 405 " ideal model delta sigma weight residual 114.40 125.57 -11.17 2.30e+00 1.89e-01 2.36e+01 ... (remaining 24035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.81: 10404 31.81 - 63.62: 329 63.62 - 95.43: 34 95.43 - 127.24: 0 127.24 - 159.05: 4 Dihedral angle restraints: 10771 sinusoidal: 4698 harmonic: 6073 Sorted by residual: dihedral pdb=" CA ASN G 62 " pdb=" C ASN G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta harmonic sigma weight residual -180.00 -127.51 -52.49 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" O4' C R 24 " pdb=" C1' C R 24 " pdb=" N1 C R 24 " pdb=" C2 C R 24 " ideal model delta sinusoidal sigma weight residual 200.00 40.95 159.05 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C R 28 " pdb=" C1' C R 28 " pdb=" N1 C R 28 " pdb=" C2 C R 28 " ideal model delta sinusoidal sigma weight residual 200.00 48.56 151.44 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 10768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2180 0.073 - 0.145: 442 0.145 - 0.218: 67 0.218 - 0.291: 13 0.291 - 0.363: 6 Chirality restraints: 2708 Sorted by residual: chirality pdb=" CG LEU H 78 " pdb=" CB LEU H 78 " pdb=" CD1 LEU H 78 " pdb=" CD2 LEU H 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB VAL B 131 " pdb=" CA VAL B 131 " pdb=" CG1 VAL B 131 " pdb=" CG2 VAL B 131 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL A 672 " pdb=" CA VAL A 672 " pdb=" CG1 VAL A 672 " pdb=" CG2 VAL A 672 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 2705 not shown) Planarity restraints: 2983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 553 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C PHE A 553 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE A 553 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS A 554 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 69 " 0.066 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO I 70 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO I 70 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO I 70 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 667 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLU A 667 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU A 667 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 668 " 0.019 2.00e-02 2.50e+03 ... (remaining 2980 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2228 2.75 - 3.29: 16154 3.29 - 3.82: 29425 3.82 - 4.36: 34951 4.36 - 4.90: 60835 Nonbonded interactions: 143593 Sorted by model distance: nonbonded pdb=" O MET B 76 " pdb=" OG SER B 231 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 202 " pdb=" OD2 ASP A 205 " model vdw 2.258 3.040 nonbonded pdb=" NH1 ARG H 54 " pdb=" OP1 U R 19 " model vdw 2.260 3.120 nonbonded pdb=" O ALA J 291 " pdb=" OG SER J 295 " model vdw 2.282 3.040 nonbonded pdb=" O ALA J 134 " pdb=" OG1 THR J 137 " model vdw 2.285 3.040 ... (remaining 143588 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 'F' and (resid 1 through 20 or resid 27 through 214)) selection = (chain 'G' and (resid 1 through 20 or resid 27 through 65 or resid 73 through 21 \ 4)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 20 or resid 27 through 65 or resid 73 through 21 \ 4)) } 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=0.50 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: 1.670 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 45.960 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.007 0.132 17756 Z= 0.322 Angle : 1.144 24.565 24046 Z= 0.615 Chirality : 0.063 0.363 2708 Planarity : 0.006 0.092 2983 Dihedral : 15.713 159.048 6854 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.06 % Allowed : 0.88 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.03 (0.16), residues: 2065 helix: -1.97 (0.15), residues: 738 sheet: -1.13 (0.26), residues: 357 loop : -2.32 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 334 HIS 0.007 0.001 HIS A 13 PHE 0.038 0.003 PHE J 296 TYR 0.041 0.003 TYR A 229 ARG 0.024 0.001 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.16689 ( 679) hydrogen bonds : angle 8.52868 ( 1983) SS BOND : bond 0.03150 ( 3) SS BOND : angle 14.98727 ( 6) covalent geometry : bond 0.00729 (17753) covalent geometry : angle 1.11926 (24040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.835 Fit side-chains REVERT: G 59 LYS cc_start: 0.7049 (tptp) cc_final: 0.6824 (tptt) outliers start: 1 outliers final: 4 residues processed: 235 average time/residue: 1.2836 time to fit residues: 342.7296 Evaluate side-chains 153 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain G residue 75 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 425 GLN A 734 ASN B 132 GLN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.142302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108680 restraints weight = 45152.767| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.14 r_work: 0.3283 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17756 Z= 0.128 Angle : 0.633 11.889 24046 Z= 0.333 Chirality : 0.043 0.183 2708 Planarity : 0.004 0.057 2983 Dihedral : 12.230 156.551 2746 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.22 % Allowed : 10.12 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.97 (0.17), residues: 2065 helix: -0.55 (0.18), residues: 746 sheet: -0.94 (0.26), residues: 362 loop : -2.04 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 735 HIS 0.002 0.001 HIS A 29 PHE 0.028 0.001 PHE J 296 TYR 0.016 0.001 TYR H 55 ARG 0.011 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 679) hydrogen bonds : angle 5.88812 ( 1983) SS BOND : bond 0.01506 ( 3) SS BOND : angle 7.10828 ( 6) covalent geometry : bond 0.00272 (17753) covalent geometry : angle 0.62282 (24040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 174 PHE cc_start: 0.8016 (m-10) cc_final: 0.7619 (m-80) REVERT: I 175 ASP cc_start: 0.7889 (t0) cc_final: 0.7615 (t0) REVERT: F 108 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7410 (mm-30) REVERT: H 153 ASP cc_start: 0.6447 (t0) cc_final: 0.6164 (OUTLIER) REVERT: H 154 ASP cc_start: 0.6609 (m-30) cc_final: 0.6026 (m-30) REVERT: A 242 TYR cc_start: 0.8732 (m-10) cc_final: 0.8530 (m-80) REVERT: A 520 ASP cc_start: 0.8646 (p0) cc_final: 0.8419 (p0) REVERT: G 59 LYS cc_start: 0.7716 (tptp) cc_final: 0.7196 (tptt) REVERT: J 310 MET cc_start: 0.2987 (OUTLIER) cc_final: 0.2742 (mtm) outliers start: 22 outliers final: 9 residues processed: 199 average time/residue: 1.1019 time to fit residues: 251.7049 Evaluate side-chains 163 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 164 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 180 HIS A 5 ASN A 45 ASN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105553 restraints weight = 42215.979| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.62 r_work: 0.3240 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17756 Z= 0.202 Angle : 0.668 12.680 24046 Z= 0.347 Chirality : 0.045 0.228 2708 Planarity : 0.004 0.042 2983 Dihedral : 12.173 161.578 2739 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.88 % Allowed : 13.16 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.61 (0.18), residues: 2065 helix: 0.00 (0.19), residues: 753 sheet: -0.95 (0.26), residues: 371 loop : -2.01 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 228 HIS 0.003 0.001 HIS F 16 PHE 0.028 0.002 PHE J 296 TYR 0.021 0.002 TYR H 55 ARG 0.007 0.001 ARG A 700 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 679) hydrogen bonds : angle 5.61494 ( 1983) SS BOND : bond 0.01813 ( 3) SS BOND : angle 7.83871 ( 6) covalent geometry : bond 0.00453 (17753) covalent geometry : angle 0.65647 (24040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.845 Fit side-chains revert: symmetry clash REVERT: I 15 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (tmm) REVERT: F 171 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8520 (mp) REVERT: H 153 ASP cc_start: 0.6582 (t0) cc_final: 0.6268 (t0) REVERT: H 154 ASP cc_start: 0.6478 (m-30) cc_final: 0.5871 (m-30) REVERT: H 157 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6427 (mp0) REVERT: A 94 GLU cc_start: 0.8336 (tt0) cc_final: 0.8028 (tt0) REVERT: A 486 MET cc_start: 0.8502 (ptp) cc_final: 0.8294 (ptp) REVERT: A 669 ASP cc_start: 0.7730 (m-30) cc_final: 0.7487 (m-30) REVERT: A 670 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6463 (mp) REVERT: B 244 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: G 59 LYS cc_start: 0.7921 (tptp) cc_final: 0.7343 (tptt) REVERT: G 120 GLU cc_start: 0.6939 (tt0) cc_final: 0.6628 (tt0) REVERT: G 133 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7201 (ptm160) REVERT: J 310 MET cc_start: 0.3404 (OUTLIER) cc_final: 0.3049 (mtm) outliers start: 52 outliers final: 18 residues processed: 200 average time/residue: 1.1235 time to fit residues: 256.3597 Evaluate side-chains 170 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 MET Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 310 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 205 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 180 HIS ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN A 530 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099202 restraints weight = 34562.434| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.61 r_work: 0.3150 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 17756 Z= 0.454 Angle : 0.890 15.000 24046 Z= 0.460 Chirality : 0.053 0.291 2708 Planarity : 0.005 0.073 2983 Dihedral : 12.689 167.780 2739 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.98 % Allowed : 14.44 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.01 (0.17), residues: 2065 helix: -0.44 (0.18), residues: 751 sheet: -1.03 (0.25), residues: 372 loop : -2.19 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 186 HIS 0.012 0.002 HIS A 13 PHE 0.030 0.003 PHE F 162 TYR 0.026 0.003 TYR H 55 ARG 0.015 0.001 ARG I 125 Details of bonding type rmsd hydrogen bonds : bond 0.05409 ( 679) hydrogen bonds : angle 6.14779 ( 1983) SS BOND : bond 0.02642 ( 3) SS BOND : angle 9.42571 ( 6) covalent geometry : bond 0.01036 (17753) covalent geometry : angle 0.87717 (24040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 155 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 90 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7169 (mtm-85) REVERT: I 174 PHE cc_start: 0.8168 (m-10) cc_final: 0.7911 (m-80) REVERT: F 171 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8814 (mp) REVERT: H 74 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: H 153 ASP cc_start: 0.7207 (t0) cc_final: 0.6868 (t0) REVERT: A 669 ASP cc_start: 0.7885 (m-30) cc_final: 0.7632 (m-30) REVERT: B 132 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: G 59 LYS cc_start: 0.8428 (tptp) cc_final: 0.8171 (mmmm) REVERT: G 120 GLU cc_start: 0.7318 (tt0) cc_final: 0.6996 (tt0) REVERT: G 133 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7562 (ptm160) REVERT: J 196 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6050 (mp0) REVERT: J 227 LYS cc_start: 0.4661 (mmtp) cc_final: 0.3276 (tptm) outliers start: 90 outliers final: 38 residues processed: 223 average time/residue: 1.1043 time to fit residues: 283.1326 Evaluate side-chains 175 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 90 ARG Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 225 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 193 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 530 ASN A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.139428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106064 restraints weight = 34277.148| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.52 r_work: 0.3275 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17756 Z= 0.122 Angle : 0.605 11.756 24046 Z= 0.316 Chirality : 0.043 0.263 2708 Planarity : 0.004 0.045 2983 Dihedral : 12.212 158.150 2739 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 3.10 % Allowed : 17.70 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.46 (0.18), residues: 2065 helix: 0.22 (0.19), residues: 749 sheet: -0.94 (0.26), residues: 365 loop : -1.95 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 735 HIS 0.005 0.001 HIS J 223 PHE 0.027 0.001 PHE J 296 TYR 0.050 0.001 TYR J 225 ARG 0.007 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 679) hydrogen bonds : angle 5.38740 ( 1983) SS BOND : bond 0.01328 ( 3) SS BOND : angle 7.28282 ( 6) covalent geometry : bond 0.00259 (17753) covalent geometry : angle 0.59440 (24040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: I 174 PHE cc_start: 0.8083 (m-10) cc_final: 0.7835 (m-80) REVERT: I 175 ASP cc_start: 0.7766 (t0) cc_final: 0.7524 (t0) REVERT: F 108 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: H 153 ASP cc_start: 0.6933 (t0) cc_final: 0.6590 (t0) REVERT: A 52 ILE cc_start: 0.9058 (mt) cc_final: 0.8852 (mm) REVERT: A 249 MET cc_start: 0.8919 (tpp) cc_final: 0.8651 (tpt) REVERT: A 356 ASP cc_start: 0.7862 (t0) cc_final: 0.7496 (t0) REVERT: A 589 ASP cc_start: 0.8337 (m-30) cc_final: 0.8134 (m-30) REVERT: A 669 ASP cc_start: 0.7745 (m-30) cc_final: 0.7537 (m-30) REVERT: G 120 GLU cc_start: 0.6847 (tt0) cc_final: 0.6558 (tt0) REVERT: G 133 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7367 (ptm160) REVERT: J 157 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6593 (mt0) REVERT: J 196 GLU cc_start: 0.6637 (mm-30) cc_final: 0.5998 (mp0) REVERT: J 206 GLU cc_start: 0.1688 (OUTLIER) cc_final: 0.1161 (tm-30) REVERT: J 221 TYR cc_start: 0.4805 (t80) cc_final: 0.4548 (t80) REVERT: J 227 LYS cc_start: 0.4271 (mmtp) cc_final: 0.3119 (tptt) outliers start: 56 outliers final: 21 residues processed: 215 average time/residue: 1.0747 time to fit residues: 265.7455 Evaluate side-chains 176 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 206 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105233 restraints weight = 45234.855| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.27 r_work: 0.3164 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17756 Z= 0.227 Angle : 0.675 12.783 24046 Z= 0.350 Chirality : 0.046 0.204 2708 Planarity : 0.004 0.082 2983 Dihedral : 12.222 163.345 2739 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.48 % Allowed : 19.14 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.47 (0.18), residues: 2065 helix: 0.23 (0.19), residues: 750 sheet: -0.96 (0.26), residues: 368 loop : -1.97 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 186 HIS 0.005 0.001 HIS A 13 PHE 0.029 0.002 PHE A 728 TYR 0.026 0.002 TYR J 221 ARG 0.014 0.001 ARG I 125 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 679) hydrogen bonds : angle 5.52034 ( 1983) SS BOND : bond 0.01830 ( 3) SS BOND : angle 8.01151 ( 6) covalent geometry : bond 0.00514 (17753) covalent geometry : angle 0.66305 (24040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 1.965 Fit side-chains revert: symmetry clash REVERT: I 173 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: F 108 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: F 136 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: H 74 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6687 (mp10) REVERT: H 153 ASP cc_start: 0.7017 (t0) cc_final: 0.6621 (t0) REVERT: H 154 ASP cc_start: 0.6737 (m-30) cc_final: 0.6178 (m-30) REVERT: H 175 ASP cc_start: 0.8447 (t70) cc_final: 0.8186 (t70) REVERT: A 52 ILE cc_start: 0.9139 (mt) cc_final: 0.8919 (mm) REVERT: A 181 MET cc_start: 0.8960 (tmm) cc_final: 0.8667 (ttt) REVERT: A 356 ASP cc_start: 0.7996 (t0) cc_final: 0.7648 (t0) REVERT: A 503 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8149 (ttp) REVERT: B 132 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: G 53 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8969 (mtp) REVERT: G 120 GLU cc_start: 0.7082 (tt0) cc_final: 0.6640 (tt0) REVERT: G 133 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7392 (ptm160) REVERT: J 157 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6785 (mt0) REVERT: J 196 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6431 (mp0) REVERT: J 206 GLU cc_start: 0.1609 (OUTLIER) cc_final: 0.1228 (tm-30) REVERT: J 227 LYS cc_start: 0.4144 (mmtp) cc_final: 0.2963 (tptm) outliers start: 63 outliers final: 28 residues processed: 210 average time/residue: 1.0179 time to fit residues: 246.2965 Evaluate side-chains 180 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 46 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 180 HIS A 45 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104685 restraints weight = 37723.214| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.99 r_work: 0.3141 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17756 Z= 0.279 Angle : 0.721 13.390 24046 Z= 0.373 Chirality : 0.047 0.209 2708 Planarity : 0.004 0.069 2983 Dihedral : 12.394 167.602 2739 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.71 % Allowed : 19.86 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.61 (0.18), residues: 2065 helix: 0.06 (0.19), residues: 753 sheet: -1.07 (0.25), residues: 374 loop : -2.00 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.007 0.001 HIS A 13 PHE 0.027 0.002 PHE J 296 TYR 0.023 0.002 TYR H 55 ARG 0.010 0.001 ARG I 125 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 679) hydrogen bonds : angle 5.66668 ( 1983) SS BOND : bond 0.01992 ( 3) SS BOND : angle 8.33774 ( 6) covalent geometry : bond 0.00633 (17753) covalent geometry : angle 0.70940 (24040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 152 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 173 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: I 174 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: I 175 ASP cc_start: 0.7957 (t0) cc_final: 0.7588 (t0) REVERT: I 211 ILE cc_start: 0.5494 (pt) cc_final: 0.5285 (pt) REVERT: F 108 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: F 136 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: H 153 ASP cc_start: 0.7020 (t0) cc_final: 0.6791 (t0) REVERT: A 356 ASP cc_start: 0.8029 (t0) cc_final: 0.7725 (t0) REVERT: A 503 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8204 (ttp) REVERT: B 132 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.6768 (tt0) REVERT: G 1 MET cc_start: 0.8324 (ptp) cc_final: 0.8096 (ptm) REVERT: G 53 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.9033 (mtp) REVERT: G 120 GLU cc_start: 0.7134 (tt0) cc_final: 0.6738 (tt0) REVERT: G 133 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7360 (ptm160) REVERT: J 196 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6604 (mp0) REVERT: J 206 GLU cc_start: 0.1432 (OUTLIER) cc_final: 0.1100 (tm-30) outliers start: 67 outliers final: 34 residues processed: 206 average time/residue: 1.0757 time to fit residues: 255.0299 Evaluate side-chains 184 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 174 PHE Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 165 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 3 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 180 HIS A 45 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.137506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.103718 restraints weight = 44813.474| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.02 r_work: 0.3208 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17756 Z= 0.156 Angle : 0.632 12.394 24046 Z= 0.327 Chirality : 0.044 0.194 2708 Planarity : 0.004 0.080 2983 Dihedral : 12.204 163.624 2739 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.26 % Allowed : 20.96 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.36 (0.18), residues: 2065 helix: 0.32 (0.19), residues: 756 sheet: -1.01 (0.26), residues: 357 loop : -1.87 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 228 HIS 0.003 0.001 HIS A 13 PHE 0.032 0.001 PHE A 728 TYR 0.021 0.001 TYR H 55 ARG 0.008 0.000 ARG I 125 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 679) hydrogen bonds : angle 5.39561 ( 1983) SS BOND : bond 0.01455 ( 3) SS BOND : angle 7.73576 ( 6) covalent geometry : bond 0.00346 (17753) covalent geometry : angle 0.62023 (24040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 159 time to evaluate : 2.007 Fit side-chains revert: symmetry clash REVERT: I 173 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: I 174 PHE cc_start: 0.8151 (m-80) cc_final: 0.7829 (m-80) REVERT: I 175 ASP cc_start: 0.7790 (t0) cc_final: 0.7476 (t0) REVERT: I 211 ILE cc_start: 0.5485 (pt) cc_final: 0.5277 (pt) REVERT: F 108 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7225 (tp30) REVERT: F 116 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: H 74 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6653 (mp10) REVERT: H 153 ASP cc_start: 0.6861 (t0) cc_final: 0.6587 (t0) REVERT: A 356 ASP cc_start: 0.7957 (t0) cc_final: 0.7603 (t0) REVERT: A 453 MET cc_start: 0.8479 (ttp) cc_final: 0.8187 (mtp) REVERT: G 120 GLU cc_start: 0.7014 (tt0) cc_final: 0.6782 (tt0) REVERT: G 133 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7679 (pmm-80) REVERT: G 147 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: J 157 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6555 (mt0) REVERT: J 196 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6580 (mp0) REVERT: J 206 GLU cc_start: 0.1477 (OUTLIER) cc_final: 0.1202 (tm-30) REVERT: J 227 LYS cc_start: 0.4047 (mmtp) cc_final: 0.2910 (tptm) REVERT: J 270 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.5556 (tt) outliers start: 59 outliers final: 30 residues processed: 206 average time/residue: 1.0576 time to fit residues: 252.3055 Evaluate side-chains 186 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 180 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110164 restraints weight = 44217.908| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.15 r_work: 0.3280 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17756 Z= 0.155 Angle : 0.632 12.130 24046 Z= 0.326 Chirality : 0.044 0.202 2708 Planarity : 0.004 0.077 2983 Dihedral : 12.111 164.088 2739 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.77 % Allowed : 21.85 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.26 (0.18), residues: 2065 helix: 0.42 (0.19), residues: 757 sheet: -0.95 (0.25), residues: 363 loop : -1.84 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 228 HIS 0.003 0.001 HIS A 13 PHE 0.026 0.001 PHE J 296 TYR 0.023 0.001 TYR H 55 ARG 0.012 0.000 ARG I 125 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 679) hydrogen bonds : angle 5.32824 ( 1983) SS BOND : bond 0.01441 ( 3) SS BOND : angle 7.57870 ( 6) covalent geometry : bond 0.00345 (17753) covalent geometry : angle 0.62114 (24040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 3.897 Fit side-chains revert: symmetry clash REVERT: I 173 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: I 174 PHE cc_start: 0.8125 (m-80) cc_final: 0.7804 (m-80) REVERT: I 175 ASP cc_start: 0.7704 (t0) cc_final: 0.7423 (t0) REVERT: F 108 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: F 116 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: F 120 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7353 (mt-10) REVERT: H 74 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: H 153 ASP cc_start: 0.6923 (t0) cc_final: 0.6616 (t0) REVERT: A 356 ASP cc_start: 0.7893 (t0) cc_final: 0.7541 (t0) REVERT: A 503 MET cc_start: 0.8428 (ttp) cc_final: 0.8225 (ttp) REVERT: G 120 GLU cc_start: 0.7059 (tt0) cc_final: 0.6845 (tt0) REVERT: G 147 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: J 157 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6528 (mt0) REVERT: J 196 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6413 (mp0) REVERT: J 206 GLU cc_start: 0.1494 (OUTLIER) cc_final: 0.1258 (tm-30) REVERT: J 227 LYS cc_start: 0.4138 (mmtp) cc_final: 0.2915 (tptm) REVERT: J 270 ILE cc_start: 0.6201 (OUTLIER) cc_final: 0.5432 (tt) outliers start: 50 outliers final: 30 residues processed: 188 average time/residue: 1.3667 time to fit residues: 298.0491 Evaluate side-chains 187 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 74 GLN Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4174 > 50: distance: 30 - 58: 18.181 distance: 54 - 58: 18.695 distance: 58 - 59: 9.752 distance: 59 - 60: 18.704 distance: 59 - 62: 13.056 distance: 60 - 61: 20.972 distance: 60 - 69: 11.547 distance: 62 - 63: 8.300 distance: 63 - 64: 11.789 distance: 63 - 65: 33.936 distance: 64 - 66: 6.352 distance: 65 - 67: 10.103 distance: 66 - 68: 25.217 distance: 67 - 68: 25.507 distance: 69 - 70: 18.682 distance: 70 - 71: 7.487 distance: 70 - 73: 5.870 distance: 71 - 72: 9.578 distance: 71 - 78: 8.934 distance: 73 - 74: 6.878 distance: 74 - 75: 19.593 distance: 75 - 76: 5.527 distance: 75 - 77: 30.184 distance: 78 - 79: 28.311 distance: 79 - 80: 23.728 distance: 79 - 82: 20.198 distance: 80 - 81: 3.148 distance: 80 - 87: 37.709 distance: 82 - 83: 15.407 distance: 83 - 84: 22.777 distance: 84 - 85: 9.531 distance: 87 - 88: 7.089 distance: 88 - 89: 3.653 distance: 88 - 91: 9.243 distance: 89 - 90: 8.543 distance: 89 - 98: 7.410 distance: 91 - 92: 12.652 distance: 92 - 93: 6.784 distance: 92 - 94: 11.667 distance: 93 - 95: 10.149 distance: 94 - 96: 8.698 distance: 95 - 97: 10.882 distance: 96 - 97: 9.341 distance: 98 - 99: 7.465 distance: 99 - 100: 11.166 distance: 99 - 102: 22.782 distance: 100 - 101: 16.562 distance: 100 - 109: 12.093 distance: 102 - 103: 4.469 distance: 103 - 104: 26.718 distance: 104 - 105: 37.182 distance: 105 - 106: 7.687 distance: 106 - 107: 30.503 distance: 109 - 110: 17.138 distance: 110 - 111: 10.449 distance: 110 - 113: 22.395 distance: 111 - 112: 8.816 distance: 111 - 117: 6.517 distance: 112 - 141: 20.916 distance: 113 - 114: 13.902 distance: 114 - 115: 5.646 distance: 114 - 116: 16.342 distance: 117 - 118: 12.594 distance: 118 - 119: 13.456 distance: 118 - 121: 6.922 distance: 119 - 124: 21.785 distance: 120 - 148: 15.439 distance: 124 - 125: 4.512 distance: 125 - 126: 11.325 distance: 125 - 128: 12.105 distance: 126 - 127: 6.842 distance: 126 - 133: 7.224 distance: 127 - 156: 21.720 distance: 128 - 129: 11.784 distance: 129 - 130: 7.523 distance: 130 - 131: 5.958 distance: 133 - 134: 6.789 distance: 134 - 135: 3.840 distance: 134 - 137: 15.320 distance: 135 - 136: 11.593 distance: 135 - 141: 4.149 distance: 136 - 162: 27.520 distance: 137 - 138: 11.460 distance: 138 - 139: 18.991 distance: 138 - 140: 24.016 distance: 141 - 142: 8.167 distance: 142 - 143: 14.904 distance: 142 - 145: 25.082 distance: 143 - 144: 8.822 distance: 143 - 148: 11.932 distance: 144 - 170: 17.511 distance: 145 - 146: 6.765