Starting phenix.real_space_refine on Sat Jun 14 17:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4s_25687/06_2025/7t4s_25687.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4s_25687/06_2025/7t4s_25687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4s_25687/06_2025/7t4s_25687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4s_25687/06_2025/7t4s_25687.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4s_25687/06_2025/7t4s_25687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4s_25687/06_2025/7t4s_25687.cif" } resolution = 3.1 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= 0.012 sd= 0.182 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 Ca 1 9.91 5 S 83 5.16 5 C 10444 2.51 5 N 2813 2.21 5 O 3063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16404 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5034 Classifications: {'peptide': 624} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 591} Chain breaks: 6 Chain: "B" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1804 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 207} Chain breaks: 1 Chain: "C" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 896 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 2 Chain: "D" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1359 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 821 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain breaks: 1 Chain: "F" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2883 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 338} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 951 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "K" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.58, per 1000 atoms: 0.58 Number of scatterers: 16404 At special positions: 0 Unit cell: (202.71, 140.546, 140.546, 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) Ca 1 19.99 S 83 16.00 O 3063 8.00 N 2813 7.00 C 10444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.02 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 277 " - pdb=" SG CYS F 427 " distance=2.03 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 592 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 55 " " NAG A 802 " - " ASN A 62 " " NAG A 804 " - " ASN A 192 " " NAG D 301 " - " ASN D 201 " " NAG D 302 " - " ASN D 118 " " NAG E 201 " - " ASN E 81 " " NAG F 901 " - " ASN F 157 " " NAG F 902 " - " ASN F 152 " Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.2 seconds 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 26 sheets defined 26.9% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.703A pdb=" N ALA A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 99 " --> pdb=" O CYS A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 99' Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.816A pdb=" N ASN A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.614A pdb=" N SER A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.740A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.866A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 removed outlier: 3.675A pdb=" N ARG A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.712A pdb=" N ALA A 648 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.526A pdb=" N ARG B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.571A pdb=" N GLU B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 4.201A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 3.981A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.178A pdb=" N HIS C 82 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.561A pdb=" N LYS C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.960A pdb=" N GLY D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Proline residue: D 126 - end of helix removed outlier: 3.693A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 35 through 40 Processing helix chain 'E' and resid 45 through 69 Processing helix chain 'E' and resid 73 through 79 removed outlier: 3.820A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.532A pdb=" N GLN E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 430 through 432 No H-bonds generated for 'chain 'F' and resid 430 through 432' Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'F' and resid 461 through 466 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.610A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.524A pdb=" N ASN J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.587A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 removed outlier: 5.960A pdb=" N ARG A 50 " --> pdb=" O VAL A 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 5.979A pdb=" N ALA A 75 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N PHE B 181 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS B 177 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 192 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE B 181 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN B 190 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU B 183 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 188 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.619A pdb=" N ARG A 136 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 223 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 528 removed outlier: 3.572A pdb=" N ARG A 528 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 578 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.908A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER A 652 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N TYR A 668 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 654 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 666 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU A 656 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.429A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 155 removed outlier: 5.306A pdb=" N GLY B 161 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ARG D 102 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP B 163 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 88 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG D 76 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 90 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE D 74 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR D 92 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.699A pdb=" N ASP C 45 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.271A pdb=" N ARG C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU C 104 " --> pdb=" O ARG C 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.384A pdb=" N ARG D 160 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 168 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 122 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 194 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 157 through 161 removed outlier: 6.495A pdb=" N GLY F 259 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE F 194 " --> pdb=" O GLY F 259 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER F 261 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 174 through 180 Processing sheet with id=AB4, first strand: chain 'F' and resid 279 through 280 removed outlier: 6.219A pdb=" N GLU F 423 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE F 342 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE F 425 " --> pdb=" O THR F 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 279 through 280 removed outlier: 6.219A pdb=" N GLU F 423 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE F 342 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE F 425 " --> pdb=" O THR F 340 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG F 405 " --> pdb=" O LEU F 333 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N PHE F 335 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N LEU F 403 " --> pdb=" O PHE F 335 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N THR F 337 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N LEU F 339 " --> pdb=" O HIS F 399 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N HIS F 399 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA F 341 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS F 397 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA F 343 " --> pdb=" O LEU F 395 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU F 395 " --> pdb=" O ALA F 343 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 436 through 437 removed outlier: 6.828A pdb=" N CYS F 592 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL F 498 " --> pdb=" O CYS F 592 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 436 through 437 removed outlier: 6.828A pdb=" N CYS F 592 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL F 498 " --> pdb=" O CYS F 592 " (cutoff:3.500A) removed outlier: 12.701A pdb=" N LEU F 488 " --> pdb=" O GLU F 576 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N GLU F 576 " --> pdb=" O LEU F 488 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N VAL F 490 " --> pdb=" O TYR F 574 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N TYR F 574 " --> pdb=" O VAL F 490 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N LEU F 492 " --> pdb=" O ARG F 572 " (cutoff:3.500A) removed outlier: 12.421A pdb=" N ARG F 572 " --> pdb=" O LEU F 492 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR F 494 " --> pdb=" O TYR F 570 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR F 570 " --> pdb=" O THR F 494 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY F 500 " --> pdb=" O ASP F 564 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N ASP F 564 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ILE F 502 " --> pdb=" O ARG F 562 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N ARG F 562 " --> pdb=" O ILE F 502 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLN F 504 " --> pdb=" O ILE F 560 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N ILE F 560 " --> pdb=" O GLN F 504 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER F 529 " --> pdb=" O GLN F 569 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL F 571 " --> pdb=" O SER F 527 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER F 527 " --> pdb=" O VAL F 571 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL F 573 " --> pdb=" O LYS F 525 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS F 525 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS F 523 " --> pdb=" O PRO F 575 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ARG F 577 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL F 521 " --> pdb=" O ARG F 577 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.597A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.702A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.932A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU H 106 " --> pdb=" O LEU H 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.470A pdb=" N ILE J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.844A pdb=" N ASP J 112 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.906A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.548A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5282 1.34 - 1.46: 4062 1.46 - 1.58: 7322 1.58 - 1.71: 0 1.71 - 1.83: 120 Bond restraints: 16786 Sorted by residual: bond pdb=" N ASP F 211 " pdb=" CA ASP F 211 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.49e+00 bond pdb=" N VAL A 281 " pdb=" CA VAL A 281 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.60e+00 bond pdb=" N TYR K 49 " pdb=" CA TYR K 49 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.53e+00 bond pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.44e-02 4.82e+03 6.30e+00 bond pdb=" N ALA K 50 " pdb=" CA ALA K 50 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 6.07e+00 ... (remaining 16781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 22352 1.99 - 3.97: 408 3.97 - 5.96: 32 5.96 - 7.94: 2 7.94 - 9.93: 1 Bond angle restraints: 22795 Sorted by residual: angle pdb=" C LEU K 47 " pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 123.17 118.18 4.99 1.28e+00 6.10e-01 1.52e+01 angle pdb=" CA ALA K 50 " pdb=" C ALA K 50 " pdb=" O ALA K 50 " ideal model delta sigma weight residual 121.81 117.48 4.33 1.18e+00 7.18e-01 1.35e+01 angle pdb=" CB MET F 253 " pdb=" CG MET F 253 " pdb=" SD MET F 253 " ideal model delta sigma weight residual 112.70 102.77 9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CG ARG F 239 " pdb=" CD ARG F 239 " pdb=" NE ARG F 239 " ideal model delta sigma weight residual 112.00 119.11 -7.11 2.20e+00 2.07e-01 1.04e+01 angle pdb=" C ALA K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 120.38 116.25 4.13 1.37e+00 5.33e-01 9.09e+00 ... (remaining 22790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9375 17.96 - 35.92: 627 35.92 - 53.89: 127 53.89 - 71.85: 33 71.85 - 89.81: 13 Dihedral angle restraints: 10175 sinusoidal: 4205 harmonic: 5970 Sorted by residual: dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual 93.00 159.28 -66.28 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 83 " pdb=" CB CYS D 83 " ideal model delta sinusoidal sigma weight residual -86.00 -148.39 62.39 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CA MET F 253 " pdb=" C MET F 253 " pdb=" N ALA F 254 " pdb=" CA ALA F 254 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 10172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1824 0.040 - 0.080: 522 0.080 - 0.119: 190 0.119 - 0.159: 37 0.159 - 0.199: 4 Chirality restraints: 2577 Sorted by residual: chirality pdb=" CG LEU C 56 " pdb=" CB LEU C 56 " pdb=" CD1 LEU C 56 " pdb=" CD2 LEU C 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA GLU E 84 " pdb=" N GLU E 84 " pdb=" C GLU E 84 " pdb=" CB GLU E 84 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA VAL A 281 " pdb=" N VAL A 281 " pdb=" C VAL A 281 " pdb=" CB VAL A 281 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 2574 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 226 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C TYR B 226 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR B 226 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 227 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 227 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ASN B 227 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN B 227 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 228 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 228 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ALA B 228 " -0.064 2.00e-02 2.50e+03 pdb=" O ALA B 228 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL B 229 " 0.021 2.00e-02 2.50e+03 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1533 2.74 - 3.28: 16536 3.28 - 3.82: 27055 3.82 - 4.36: 33880 4.36 - 4.90: 57289 Nonbonded interactions: 136293 Sorted by model distance: nonbonded pdb=" O SER F 155 " pdb=" OH TYR F 264 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU F 197 " pdb="CA CA F 903 " model vdw 2.222 2.510 nonbonded pdb=" OG SER K 7 " pdb=" OG1 THR K 22 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU E 84 " pdb=" O5 NAG E 201 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU E 26 " pdb=" OH TYR E 36 " model vdw 2.257 3.040 ... (remaining 136288 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.490 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16810 Z= 0.190 Angle : 0.647 9.928 22851 Z= 0.346 Chirality : 0.044 0.199 2577 Planarity : 0.006 0.078 2901 Dihedral : 13.121 89.808 6267 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1983 helix: 0.42 (0.25), residues: 426 sheet: 0.33 (0.23), residues: 516 loop : -0.45 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 100 HIS 0.008 0.001 HIS E 69 PHE 0.016 0.002 PHE F 165 TYR 0.018 0.002 TYR A 45 ARG 0.012 0.001 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 8) link_NAG-ASN : angle 2.38631 ( 24) hydrogen bonds : bond 0.15046 ( 629) hydrogen bonds : angle 7.45639 ( 1695) SS BOND : bond 0.00351 ( 16) SS BOND : angle 1.64771 ( 32) covalent geometry : bond 0.00414 (16786) covalent geometry : angle 0.64009 (22795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 THR cc_start: 0.8386 (p) cc_final: 0.8184 (p) REVERT: A 114 THR cc_start: 0.8334 (p) cc_final: 0.7471 (p) REVERT: A 193 GLN cc_start: 0.7433 (mp-120) cc_final: 0.7091 (mm-40) REVERT: A 633 THR cc_start: 0.7335 (p) cc_final: 0.7111 (m) REVERT: A 698 LEU cc_start: 0.8884 (mt) cc_final: 0.8608 (mt) REVERT: C 87 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7408 (tp40) REVERT: C 120 TYR cc_start: 0.7513 (m-80) cc_final: 0.7275 (m-80) REVERT: C 121 LEU cc_start: 0.8343 (tp) cc_final: 0.8137 (tp) REVERT: D 117 ARG cc_start: 0.7443 (tpt170) cc_final: 0.6848 (tpt170) REVERT: D 142 GLU cc_start: 0.7351 (mp0) cc_final: 0.7108 (mp0) REVERT: D 169 TYR cc_start: 0.7635 (m-80) cc_final: 0.7334 (m-80) REVERT: F 217 ASP cc_start: 0.7232 (t0) cc_final: 0.7012 (t0) REVERT: F 246 SER cc_start: 0.8579 (t) cc_final: 0.8324 (p) REVERT: F 328 TYR cc_start: 0.7304 (p90) cc_final: 0.7039 (p90) REVERT: F 436 ASN cc_start: 0.8893 (m110) cc_final: 0.8684 (m-40) REVERT: F 487 TRP cc_start: 0.7667 (p-90) cc_final: 0.7411 (p-90) REVERT: F 494 THR cc_start: 0.7754 (p) cc_final: 0.7492 (m) REVERT: H 73 ASP cc_start: 0.5943 (t0) cc_final: 0.5730 (t0) REVERT: H 84 ASN cc_start: 0.8386 (m-40) cc_final: 0.7877 (m-40) REVERT: H 87 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6775 (mtt90) REVERT: J 83 LEU cc_start: 0.7842 (tp) cc_final: 0.7613 (tp) REVERT: K 18 ARG cc_start: 0.8465 (ttt90) cc_final: 0.8228 (ttt180) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.3555 time to fit residues: 227.6258 Evaluate side-chains 395 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.4980 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 85 ASN A 187 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS A 594 GLN B 118 GLN B 203 ASN D 164 ASN D 181 HIS F 172 ASN F 276 GLN F 396 ASN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 79 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.084719 restraints weight = 29633.857| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.53 r_work: 0.2945 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 16810 Z= 0.210 Angle : 0.682 8.735 22851 Z= 0.353 Chirality : 0.046 0.217 2577 Planarity : 0.005 0.043 2901 Dihedral : 5.935 59.799 2428 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.50 % Allowed : 9.11 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1983 helix: 0.54 (0.25), residues: 427 sheet: 0.33 (0.22), residues: 533 loop : -0.30 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 94 HIS 0.008 0.001 HIS E 69 PHE 0.019 0.002 PHE E 122 TYR 0.017 0.002 TYR J 33 ARG 0.007 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 8) link_NAG-ASN : angle 2.52241 ( 24) hydrogen bonds : bond 0.05112 ( 629) hydrogen bonds : angle 5.95855 ( 1695) SS BOND : bond 0.00334 ( 16) SS BOND : angle 1.24687 ( 32) covalent geometry : bond 0.00490 (16786) covalent geometry : angle 0.67653 (22795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 430 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7223 (tp40) REVERT: A 193 GLN cc_start: 0.7774 (mp-120) cc_final: 0.7332 (mm-40) REVERT: A 243 ASP cc_start: 0.7744 (m-30) cc_final: 0.7515 (m-30) REVERT: A 619 ASP cc_start: 0.7965 (t70) cc_final: 0.7720 (t70) REVERT: A 633 THR cc_start: 0.7412 (p) cc_final: 0.6965 (m) REVERT: A 637 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.8046 (t) REVERT: A 698 LEU cc_start: 0.8983 (mt) cc_final: 0.8711 (mt) REVERT: B 102 ASP cc_start: 0.6591 (m-30) cc_final: 0.6063 (t70) REVERT: B 162 TYR cc_start: 0.8112 (m-80) cc_final: 0.7866 (m-80) REVERT: C 97 ASN cc_start: 0.8112 (m110) cc_final: 0.7831 (m-40) REVERT: C 110 ARG cc_start: 0.8451 (ppt170) cc_final: 0.7694 (ptt90) REVERT: C 121 LEU cc_start: 0.8540 (tp) cc_final: 0.8236 (tp) REVERT: D 117 ARG cc_start: 0.7784 (tpt170) cc_final: 0.7509 (tpt170) REVERT: D 159 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8083 (mp) REVERT: E 78 LYS cc_start: 0.8153 (tppt) cc_final: 0.7951 (tppt) REVERT: F 151 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8059 (mmmt) REVERT: F 217 ASP cc_start: 0.7997 (t0) cc_final: 0.7736 (t0) REVERT: F 246 SER cc_start: 0.8811 (t) cc_final: 0.8469 (p) REVERT: F 328 TYR cc_start: 0.7828 (p90) cc_final: 0.7433 (p90) REVERT: F 338 MET cc_start: 0.8230 (mtm) cc_final: 0.7840 (mpp) REVERT: F 494 THR cc_start: 0.8036 (p) cc_final: 0.7757 (m) REVERT: H 87 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7405 (mtt90) REVERT: K 6 GLN cc_start: 0.8399 (mt0) cc_final: 0.8185 (mt0) REVERT: I 101 GLN cc_start: 0.8471 (mp10) cc_final: 0.8047 (mm-40) outliers start: 27 outliers final: 20 residues processed: 441 average time/residue: 0.3543 time to fit residues: 218.2561 Evaluate side-chains 427 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 405 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 138 optimal weight: 0.0010 chunk 159 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 273 GLN D 181 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.086131 restraints weight = 29327.096| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.53 r_work: 0.2962 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16810 Z= 0.166 Angle : 0.626 10.159 22851 Z= 0.324 Chirality : 0.045 0.163 2577 Planarity : 0.004 0.042 2901 Dihedral : 5.701 58.861 2428 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.50 % Allowed : 10.67 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1983 helix: 0.71 (0.25), residues: 421 sheet: 0.40 (0.23), residues: 529 loop : -0.29 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 179 HIS 0.007 0.001 HIS E 69 PHE 0.022 0.002 PHE E 122 TYR 0.026 0.002 TYR E 52 ARG 0.007 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 8) link_NAG-ASN : angle 2.26388 ( 24) hydrogen bonds : bond 0.04473 ( 629) hydrogen bonds : angle 5.60633 ( 1695) SS BOND : bond 0.00344 ( 16) SS BOND : angle 1.18285 ( 32) covalent geometry : bond 0.00383 (16786) covalent geometry : angle 0.62049 (22795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 419 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8254 (mm) cc_final: 0.7558 (mt) REVERT: A 141 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7256 (tp40) REVERT: A 193 GLN cc_start: 0.7709 (mp-120) cc_final: 0.7265 (mm-40) REVERT: A 407 LEU cc_start: 0.7060 (mt) cc_final: 0.6833 (mt) REVERT: A 633 THR cc_start: 0.7405 (p) cc_final: 0.6925 (m) REVERT: B 162 TYR cc_start: 0.8143 (m-80) cc_final: 0.7859 (m-80) REVERT: B 182 GLU cc_start: 0.8344 (tt0) cc_final: 0.8115 (tt0) REVERT: B 268 SER cc_start: 0.8432 (m) cc_final: 0.8172 (p) REVERT: C 97 ASN cc_start: 0.8294 (m110) cc_final: 0.7994 (m-40) REVERT: C 110 ARG cc_start: 0.8525 (ppt170) cc_final: 0.7988 (ptt90) REVERT: C 121 LEU cc_start: 0.8535 (tp) cc_final: 0.8236 (tp) REVERT: D 158 LEU cc_start: 0.8524 (mt) cc_final: 0.8296 (mp) REVERT: D 159 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8003 (mp) REVERT: D 160 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7537 (mtp85) REVERT: E 78 LYS cc_start: 0.8112 (tppt) cc_final: 0.7870 (mmtm) REVERT: F 185 MET cc_start: 0.7122 (mmm) cc_final: 0.6767 (mmp) REVERT: F 217 ASP cc_start: 0.7978 (t0) cc_final: 0.7738 (t0) REVERT: F 246 SER cc_start: 0.8809 (t) cc_final: 0.8474 (p) REVERT: F 328 TYR cc_start: 0.7749 (p90) cc_final: 0.7487 (p90) outliers start: 45 outliers final: 34 residues processed: 438 average time/residue: 0.3594 time to fit residues: 219.8806 Evaluate side-chains 443 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 407 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 131 optimal weight: 0.0000 chunk 197 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 201 HIS B 203 ASN B 273 GLN D 181 HIS F 276 GLN H 111 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.086388 restraints weight = 29765.941| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.42 r_work: 0.2982 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16810 Z= 0.146 Angle : 0.598 9.244 22851 Z= 0.309 Chirality : 0.043 0.164 2577 Planarity : 0.004 0.044 2901 Dihedral : 5.435 57.625 2428 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.89 % Allowed : 11.72 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1983 helix: 0.76 (0.25), residues: 423 sheet: 0.46 (0.23), residues: 529 loop : -0.29 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 94 HIS 0.006 0.001 HIS E 69 PHE 0.021 0.002 PHE E 122 TYR 0.045 0.002 TYR E 52 ARG 0.010 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 8) link_NAG-ASN : angle 2.03606 ( 24) hydrogen bonds : bond 0.04055 ( 629) hydrogen bonds : angle 5.38578 ( 1695) SS BOND : bond 0.00280 ( 16) SS BOND : angle 1.10413 ( 32) covalent geometry : bond 0.00335 (16786) covalent geometry : angle 0.59375 (22795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 430 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8208 (mm) cc_final: 0.7598 (mt) REVERT: A 141 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7367 (tp40) REVERT: A 193 GLN cc_start: 0.7483 (mp-120) cc_final: 0.7051 (mm-40) REVERT: A 407 LEU cc_start: 0.7050 (mt) cc_final: 0.6801 (mt) REVERT: A 458 PHE cc_start: 0.8603 (p90) cc_final: 0.8339 (p90) REVERT: A 466 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 696 MET cc_start: 0.8188 (tpp) cc_final: 0.7909 (ttm) REVERT: B 148 SER cc_start: 0.6927 (t) cc_final: 0.6707 (t) REVERT: B 162 TYR cc_start: 0.8138 (m-80) cc_final: 0.7830 (m-80) REVERT: B 268 SER cc_start: 0.8374 (m) cc_final: 0.8100 (p) REVERT: C 97 ASN cc_start: 0.8338 (m110) cc_final: 0.8047 (m-40) REVERT: C 110 ARG cc_start: 0.8458 (ppt170) cc_final: 0.8036 (ptt90) REVERT: C 121 LEU cc_start: 0.8489 (tp) cc_final: 0.8179 (tp) REVERT: D 159 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8034 (mp) REVERT: D 160 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7507 (mtp85) REVERT: E 78 LYS cc_start: 0.8103 (tppt) cc_final: 0.7850 (mmtm) REVERT: F 185 MET cc_start: 0.7057 (mmm) cc_final: 0.6683 (mmt) REVERT: F 190 GLN cc_start: 0.8766 (mt0) cc_final: 0.8456 (mt0) REVERT: F 217 ASP cc_start: 0.7897 (t0) cc_final: 0.7691 (t0) REVERT: F 246 SER cc_start: 0.8750 (t) cc_final: 0.8372 (p) REVERT: F 328 TYR cc_start: 0.7678 (p90) cc_final: 0.7447 (p90) REVERT: F 373 MET cc_start: 0.8383 (ttp) cc_final: 0.8056 (ttp) REVERT: F 392 GLU cc_start: 0.7562 (mp0) cc_final: 0.7272 (mp0) REVERT: H 87 ARG cc_start: 0.7487 (mtt90) cc_final: 0.7282 (mtt-85) outliers start: 52 outliers final: 37 residues processed: 459 average time/residue: 0.3575 time to fit residues: 228.6854 Evaluate side-chains 455 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 416 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 178 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 331 GLN B 203 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS F 276 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** 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 = 0.3313 r_free = 0.3313 target = 0.099322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.085851 restraints weight = 30339.433| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.44 r_work: 0.2971 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16810 Z= 0.166 Angle : 0.614 8.742 22851 Z= 0.316 Chirality : 0.044 0.172 2577 Planarity : 0.005 0.045 2901 Dihedral : 5.407 58.208 2428 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.00 % Allowed : 13.39 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1983 helix: 0.78 (0.25), residues: 423 sheet: 0.44 (0.23), residues: 529 loop : -0.31 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 94 HIS 0.007 0.001 HIS E 69 PHE 0.017 0.002 PHE E 122 TYR 0.059 0.002 TYR E 52 ARG 0.011 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 8) link_NAG-ASN : angle 2.02932 ( 24) hydrogen bonds : bond 0.04114 ( 629) hydrogen bonds : angle 5.36263 ( 1695) SS BOND : bond 0.00368 ( 16) SS BOND : angle 1.05619 ( 32) covalent geometry : bond 0.00385 (16786) covalent geometry : angle 0.60982 (22795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 430 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8204 (mm) cc_final: 0.7585 (mt) REVERT: A 141 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7400 (tp40) REVERT: A 193 GLN cc_start: 0.7455 (mp-120) cc_final: 0.7028 (mm-40) REVERT: A 407 LEU cc_start: 0.7064 (mt) cc_final: 0.6806 (mt) REVERT: A 466 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 696 MET cc_start: 0.8176 (tpp) cc_final: 0.7776 (ttm) REVERT: B 113 TYR cc_start: 0.8238 (t80) cc_final: 0.7833 (t80) REVERT: B 148 SER cc_start: 0.6967 (t) cc_final: 0.6763 (t) REVERT: B 162 TYR cc_start: 0.8196 (m-80) cc_final: 0.7862 (m-80) REVERT: B 268 SER cc_start: 0.8331 (m) cc_final: 0.8072 (p) REVERT: C 97 ASN cc_start: 0.8350 (m110) cc_final: 0.8065 (m-40) REVERT: C 110 ARG cc_start: 0.8501 (ppt170) cc_final: 0.8097 (ptt90) REVERT: C 121 LEU cc_start: 0.8474 (tp) cc_final: 0.8215 (tp) REVERT: C 130 TYR cc_start: 0.8294 (p90) cc_final: 0.7994 (p90) REVERT: D 158 LEU cc_start: 0.8544 (mt) cc_final: 0.8324 (mp) REVERT: D 160 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7506 (mtp85) REVERT: E 78 LYS cc_start: 0.8110 (tppt) cc_final: 0.7831 (mmtm) REVERT: F 185 MET cc_start: 0.6995 (mmm) cc_final: 0.6556 (mmt) REVERT: F 190 GLN cc_start: 0.8762 (mt0) cc_final: 0.8379 (mt0) REVERT: F 246 SER cc_start: 0.8710 (t) cc_final: 0.8318 (p) REVERT: F 328 TYR cc_start: 0.7686 (p90) cc_final: 0.7442 (p90) REVERT: F 518 ARG cc_start: 0.8079 (mpp80) cc_final: 0.7849 (mtm-85) REVERT: I 42 GLN cc_start: 0.7808 (mp10) cc_final: 0.7511 (mp10) outliers start: 54 outliers final: 45 residues processed: 457 average time/residue: 0.3365 time to fit residues: 214.6690 Evaluate side-chains 468 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 422 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 184 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 107 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** 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 = 0.3301 r_free = 0.3301 target = 0.098598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085105 restraints weight = 29952.488| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.43 r_work: 0.2955 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16810 Z= 0.201 Angle : 0.646 8.746 22851 Z= 0.334 Chirality : 0.045 0.176 2577 Planarity : 0.005 0.055 2901 Dihedral : 5.537 59.509 2428 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.44 % Allowed : 13.83 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1983 helix: 0.68 (0.25), residues: 423 sheet: 0.41 (0.23), residues: 531 loop : -0.37 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 94 HIS 0.008 0.001 HIS E 69 PHE 0.023 0.002 PHE E 122 TYR 0.074 0.002 TYR E 52 ARG 0.013 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 8) link_NAG-ASN : angle 1.99518 ( 24) hydrogen bonds : bond 0.04355 ( 629) hydrogen bonds : angle 5.42660 ( 1695) SS BOND : bond 0.00465 ( 16) SS BOND : angle 1.41407 ( 32) covalent geometry : bond 0.00466 (16786) covalent geometry : angle 0.64100 (22795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 430 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8245 (mm) cc_final: 0.7642 (mt) REVERT: A 141 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7415 (tp40) REVERT: A 193 GLN cc_start: 0.7450 (mp-120) cc_final: 0.7019 (mm-40) REVERT: A 407 LEU cc_start: 0.7060 (mt) cc_final: 0.6825 (mt) REVERT: A 466 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 633 THR cc_start: 0.7403 (p) cc_final: 0.6935 (m) REVERT: B 268 SER cc_start: 0.8322 (m) cc_final: 0.8076 (p) REVERT: C 43 CYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6226 (p) REVERT: C 97 ASN cc_start: 0.8400 (m110) cc_final: 0.8139 (m-40) REVERT: C 110 ARG cc_start: 0.8500 (ppt170) cc_final: 0.8106 (ptt90) REVERT: C 121 LEU cc_start: 0.8495 (tp) cc_final: 0.8207 (tp) REVERT: C 130 TYR cc_start: 0.8280 (p90) cc_final: 0.8053 (p90) REVERT: D 160 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7490 (mtp85) REVERT: E 78 LYS cc_start: 0.8122 (tppt) cc_final: 0.7838 (mmtm) REVERT: F 190 GLN cc_start: 0.8773 (mt0) cc_final: 0.8397 (mt0) REVERT: F 246 SER cc_start: 0.8673 (t) cc_final: 0.8289 (p) REVERT: F 328 TYR cc_start: 0.7745 (p90) cc_final: 0.7524 (p90) REVERT: F 518 ARG cc_start: 0.8073 (mpp80) cc_final: 0.7865 (mtm-85) REVERT: I 42 GLN cc_start: 0.7832 (mp10) cc_final: 0.7530 (mp10) outliers start: 62 outliers final: 50 residues processed: 464 average time/residue: 0.3434 time to fit residues: 223.7015 Evaluate side-chains 474 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 422 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 107 ASN A 187 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS F 276 GLN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085708 restraints weight = 30065.019| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.43 r_work: 0.2964 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16810 Z= 0.167 Angle : 0.630 9.926 22851 Z= 0.324 Chirality : 0.044 0.164 2577 Planarity : 0.005 0.062 2901 Dihedral : 5.442 58.012 2428 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.39 % Allowed : 15.22 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1983 helix: 0.71 (0.25), residues: 422 sheet: 0.40 (0.23), residues: 532 loop : -0.33 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 94 HIS 0.006 0.001 HIS E 69 PHE 0.018 0.002 PHE E 122 TYR 0.065 0.002 TYR E 52 ARG 0.013 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 8) link_NAG-ASN : angle 1.93697 ( 24) hydrogen bonds : bond 0.04071 ( 629) hydrogen bonds : angle 5.35519 ( 1695) SS BOND : bond 0.00327 ( 16) SS BOND : angle 1.23682 ( 32) covalent geometry : bond 0.00386 (16786) covalent geometry : angle 0.62542 (22795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 428 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8107 (mm) cc_final: 0.7478 (mt) REVERT: A 141 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7414 (tp40) REVERT: A 193 GLN cc_start: 0.7408 (mp-120) cc_final: 0.6973 (mm-40) REVERT: A 330 CYS cc_start: 0.7670 (t) cc_final: 0.7238 (m) REVERT: A 407 LEU cc_start: 0.7051 (mt) cc_final: 0.6813 (mt) REVERT: A 466 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 564 GLU cc_start: 0.8075 (pp20) cc_final: 0.7834 (pp20) REVERT: B 113 TYR cc_start: 0.8281 (t80) cc_final: 0.7812 (t80) REVERT: B 162 TYR cc_start: 0.8165 (m-80) cc_final: 0.7964 (m-80) REVERT: B 268 SER cc_start: 0.8336 (m) cc_final: 0.8030 (p) REVERT: C 43 CYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6220 (p) REVERT: C 97 ASN cc_start: 0.8394 (m110) cc_final: 0.8135 (m-40) REVERT: C 110 ARG cc_start: 0.8506 (ppt170) cc_final: 0.8111 (ptt90) REVERT: C 121 LEU cc_start: 0.8486 (tp) cc_final: 0.8172 (tp) REVERT: C 130 TYR cc_start: 0.8272 (p90) cc_final: 0.8046 (p90) REVERT: D 160 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7448 (mtp85) REVERT: E 78 LYS cc_start: 0.8119 (tppt) cc_final: 0.7847 (mmtm) REVERT: F 185 MET cc_start: 0.7091 (mmm) cc_final: 0.6803 (mmt) REVERT: F 190 GLN cc_start: 0.8752 (mt0) cc_final: 0.8426 (mt0) REVERT: F 246 SER cc_start: 0.8582 (t) cc_final: 0.8265 (p) REVERT: J 45 LEU cc_start: 0.8954 (mt) cc_final: 0.8592 (mt) REVERT: I 42 GLN cc_start: 0.7872 (mp10) cc_final: 0.7564 (mp10) outliers start: 61 outliers final: 53 residues processed: 462 average time/residue: 0.4303 time to fit residues: 280.7764 Evaluate side-chains 478 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 423 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 69 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 107 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** 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 = 0.3277 r_free = 0.3277 target = 0.097189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083394 restraints weight = 30060.028| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.44 r_work: 0.2923 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16810 Z= 0.292 Angle : 0.731 9.738 22851 Z= 0.377 Chirality : 0.048 0.176 2577 Planarity : 0.006 0.064 2901 Dihedral : 5.846 59.760 2428 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.94 % Allowed : 14.61 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1983 helix: 0.29 (0.25), residues: 428 sheet: 0.34 (0.23), residues: 535 loop : -0.50 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 94 HIS 0.010 0.002 HIS E 69 PHE 0.019 0.003 PHE B 222 TYR 0.062 0.002 TYR E 52 ARG 0.015 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 8) link_NAG-ASN : angle 2.14027 ( 24) hydrogen bonds : bond 0.04883 ( 629) hydrogen bonds : angle 5.63521 ( 1695) SS BOND : bond 0.00493 ( 16) SS BOND : angle 1.39581 ( 32) covalent geometry : bond 0.00680 (16786) covalent geometry : angle 0.72622 (22795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 426 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8133 (mm) cc_final: 0.7492 (mt) REVERT: A 110 ASP cc_start: 0.8031 (t0) cc_final: 0.7767 (t0) REVERT: A 193 GLN cc_start: 0.7443 (mp-120) cc_final: 0.7013 (mm-40) REVERT: A 330 CYS cc_start: 0.7791 (t) cc_final: 0.7389 (m) REVERT: A 407 LEU cc_start: 0.7098 (mt) cc_final: 0.6854 (mt) REVERT: A 466 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 268 SER cc_start: 0.8767 (m) cc_final: 0.8446 (p) REVERT: C 43 CYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6313 (p) REVERT: C 97 ASN cc_start: 0.8463 (m110) cc_final: 0.8100 (m-40) REVERT: C 110 ARG cc_start: 0.8544 (ppt170) cc_final: 0.8142 (ptt90) REVERT: C 121 LEU cc_start: 0.8493 (tp) cc_final: 0.8204 (tp) REVERT: D 160 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7513 (mtp85) REVERT: E 78 LYS cc_start: 0.8119 (tppt) cc_final: 0.7853 (mmtm) REVERT: F 185 MET cc_start: 0.7169 (mmm) cc_final: 0.6910 (mmt) REVERT: F 190 GLN cc_start: 0.8806 (mt0) cc_final: 0.8475 (mt0) REVERT: F 246 SER cc_start: 0.8585 (t) cc_final: 0.8272 (p) REVERT: I 42 GLN cc_start: 0.7950 (mp10) cc_final: 0.7678 (mp10) outliers start: 71 outliers final: 61 residues processed: 465 average time/residue: 0.3896 time to fit residues: 252.1633 Evaluate side-chains 484 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 421 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 187 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN C 90 HIS ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 181 HIS F 276 GLN H 82 GLN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.085325 restraints weight = 29744.329| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.54 r_work: 0.2949 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16810 Z= 0.163 Angle : 0.636 9.035 22851 Z= 0.329 Chirality : 0.044 0.165 2577 Planarity : 0.005 0.053 2901 Dihedral : 5.507 57.628 2428 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.50 % Allowed : 16.06 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1983 helix: 0.62 (0.25), residues: 422 sheet: 0.33 (0.23), residues: 540 loop : -0.42 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 94 HIS 0.006 0.001 HIS E 69 PHE 0.020 0.002 PHE E 122 TYR 0.056 0.002 TYR E 52 ARG 0.015 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 8) link_NAG-ASN : angle 1.94511 ( 24) hydrogen bonds : bond 0.04035 ( 629) hydrogen bonds : angle 5.36537 ( 1695) SS BOND : bond 0.00328 ( 16) SS BOND : angle 1.07596 ( 32) covalent geometry : bond 0.00378 (16786) covalent geometry : angle 0.63223 (22795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 424 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8088 (mm) cc_final: 0.7398 (mt) REVERT: A 110 ASP cc_start: 0.8009 (t0) cc_final: 0.7713 (t0) REVERT: A 193 GLN cc_start: 0.7358 (mp-120) cc_final: 0.6923 (mm-40) REVERT: A 330 CYS cc_start: 0.7726 (t) cc_final: 0.7374 (m) REVERT: A 407 LEU cc_start: 0.7045 (mt) cc_final: 0.6794 (mt) REVERT: A 466 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 585 GLU cc_start: 0.7509 (pm20) cc_final: 0.7072 (pm20) REVERT: B 268 SER cc_start: 0.8750 (m) cc_final: 0.8404 (p) REVERT: C 43 CYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6291 (p) REVERT: C 97 ASN cc_start: 0.8408 (m110) cc_final: 0.8162 (m-40) REVERT: C 110 ARG cc_start: 0.8494 (ppt170) cc_final: 0.8107 (ptt90) REVERT: C 121 LEU cc_start: 0.8521 (tp) cc_final: 0.8214 (tp) REVERT: D 160 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7547 (mtp85) REVERT: E 78 LYS cc_start: 0.8158 (tppt) cc_final: 0.7881 (mmtm) REVERT: F 185 MET cc_start: 0.7158 (mmm) cc_final: 0.6903 (mmt) REVERT: F 246 SER cc_start: 0.8576 (t) cc_final: 0.8267 (p) REVERT: F 536 GLU cc_start: 0.7425 (mp0) cc_final: 0.7201 (mp0) REVERT: J 45 LEU cc_start: 0.8938 (mt) cc_final: 0.8583 (mt) REVERT: I 21 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8426 (mp) REVERT: I 42 GLN cc_start: 0.7955 (mp10) cc_final: 0.7628 (mp10) outliers start: 63 outliers final: 52 residues processed: 457 average time/residue: 0.3573 time to fit residues: 228.3927 Evaluate side-chains 477 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 422 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 29 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 181 HIS F 276 GLN J 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.084514 restraints weight = 29821.023| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.55 r_work: 0.2926 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16810 Z= 0.217 Angle : 0.681 12.181 22851 Z= 0.350 Chirality : 0.045 0.165 2577 Planarity : 0.005 0.054 2901 Dihedral : 5.604 58.949 2428 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.72 % Allowed : 15.94 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1983 helix: 0.47 (0.25), residues: 428 sheet: 0.31 (0.23), residues: 539 loop : -0.47 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 94 HIS 0.008 0.001 HIS E 69 PHE 0.019 0.002 PHE E 122 TYR 0.054 0.002 TYR E 52 ARG 0.016 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 1.94637 ( 24) hydrogen bonds : bond 0.04338 ( 629) hydrogen bonds : angle 5.43436 ( 1695) SS BOND : bond 0.00383 ( 16) SS BOND : angle 1.16460 ( 32) covalent geometry : bond 0.00507 (16786) covalent geometry : angle 0.67793 (22795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3966 Ramachandran restraints generated. 1983 Oldfield, 0 Emsley, 1983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 420 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8121 (mm) cc_final: 0.7448 (mt) REVERT: A 110 ASP cc_start: 0.8023 (t0) cc_final: 0.7755 (t0) REVERT: A 193 GLN cc_start: 0.7386 (mp-120) cc_final: 0.6961 (mm-40) REVERT: A 330 CYS cc_start: 0.7788 (t) cc_final: 0.7410 (m) REVERT: A 407 LEU cc_start: 0.7088 (mt) cc_final: 0.6851 (mt) REVERT: A 466 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 268 SER cc_start: 0.8748 (m) cc_final: 0.8409 (p) REVERT: C 43 CYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6337 (p) REVERT: C 97 ASN cc_start: 0.8419 (m110) cc_final: 0.8177 (m-40) REVERT: C 110 ARG cc_start: 0.8522 (ppt170) cc_final: 0.8151 (ptt90) REVERT: C 121 LEU cc_start: 0.8529 (tp) cc_final: 0.8235 (tp) REVERT: D 160 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7544 (mtp85) REVERT: E 78 LYS cc_start: 0.8136 (tppt) cc_final: 0.7872 (mmtm) REVERT: F 185 MET cc_start: 0.7223 (mmm) cc_final: 0.6970 (mmt) REVERT: F 246 SER cc_start: 0.8575 (t) cc_final: 0.8269 (p) REVERT: J 45 LEU cc_start: 0.8943 (mt) cc_final: 0.8594 (mt) REVERT: K 79 GLN cc_start: 0.8578 (mm110) cc_final: 0.8364 (mm110) REVERT: I 21 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8436 (mp) REVERT: I 42 GLN cc_start: 0.7987 (mp10) cc_final: 0.7667 (mp10) outliers start: 67 outliers final: 58 residues processed: 456 average time/residue: 0.3648 time to fit residues: 234.2893 Evaluate side-chains 482 residues out of total 1801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 421 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 460 TRP Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS B 197 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS F 276 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085640 restraints weight = 29744.236| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.54 r_work: 0.2936 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16810 Z= 0.158 Angle : 0.640 11.055 22851 Z= 0.330 Chirality : 0.044 0.161 2577 Planarity : 0.005 0.048 2901 Dihedral : 5.461 57.224 2428 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.33 % Allowed : 16.50 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1983 helix: 0.64 (0.25), residues: 423 sheet: 0.33 (0.23), residues: 539 loop : -0.42 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 94 HIS 0.006 0.001 HIS E 69 PHE 0.019 0.002 PHE E 122 TYR 0.052 0.002 TYR E 52 ARG 0.017 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 8) link_NAG-ASN : angle 1.85547 ( 24) hydrogen bonds : bond 0.04003 ( 629) hydrogen bonds : angle 5.32503 ( 1695) SS BOND : bond 0.00309 ( 16) SS BOND : angle 1.03358 ( 32) covalent geometry : bond 0.00368 (16786) covalent geometry : angle 0.63725 (22795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11269.72 seconds wall clock time: 197 minutes 28.90 seconds (11848.90 seconds total)