Starting phenix.real_space_refine on Sun Jun 22 09:46:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcg_38242/06_2025/8xcg_38242.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcg_38242/06_2025/8xcg_38242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcg_38242/06_2025/8xcg_38242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcg_38242/06_2025/8xcg_38242.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcg_38242/06_2025/8xcg_38242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcg_38242/06_2025/8xcg_38242.cif" } resolution = 3.46 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= 0.004 sd= 0.067 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 Fe 12 7.16 5 S 138 5.16 5 C 16228 2.51 5 N 4523 2.21 5 O 5040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25941 Number of models: 1 Model: "" Number of chains: 18 Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4627 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 29, 'TRANS': 564} Chain: "I" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 412 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "J" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4657 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 30, 'TRANS': 567} Chain: "K" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "P" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 436 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "Y" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "Z" Number of atoms: 4650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4650 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 29, 'TRANS': 567} Chain: "e" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "f" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "h" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 428 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12891 SG CYS L 182 91.577 90.470 69.286 1.00 27.16 S ATOM 13062 SG CYS L 205 85.408 91.943 69.478 1.00 51.17 S ATOM 12813 SG CYS L 173 86.791 86.108 68.475 1.00 33.95 S ATOM 13107 SG CYS L 212 87.012 90.562 63.982 1.00 30.13 S ATOM 15576 SG CYS N 182 19.092 62.735 71.304 1.00 53.53 S ATOM 15747 SG CYS N 205 20.398 56.107 71.928 1.00 52.32 S ATOM 15498 SG CYS N 173 24.752 60.179 70.357 1.00 53.47 S ATOM 15792 SG CYS N 212 20.597 58.204 66.112 1.00 40.06 S ATOM 24231 SG CYS f 182 79.850 13.948 75.535 1.00 68.04 S ATOM 24402 SG CYS f 205 84.408 18.820 75.651 1.00 77.47 S ATOM 24153 SG CYS f 173 78.655 20.090 73.384 1.00 75.88 S ATOM 24447 SG CYS f 212 82.450 17.327 69.805 1.00 69.39 S Time building chain proxies: 14.50, per 1000 atoms: 0.56 Number of scatterers: 25941 At special positions: 0 Unit cell: (129.978, 127.83, 166.501, 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) Fe 12 26.01 S 138 16.00 O 5040 8.00 N 4523 7.00 C 16228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 343 " - pdb=" SG CYS F 348 " distance=2.16 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 348 " distance=2.09 Simple disulfide: pdb=" SG CYS Z 343 " - pdb=" SG CYS Z 348 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.65 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 L 301 " pdb="FE1 SF4 L 301 " - pdb=" SG CYS L 182 " pdb="FE4 SF4 L 301 " - pdb=" SG CYS L 212 " pdb="FE2 SF4 L 301 " - pdb=" SG CYS L 205 " pdb="FE3 SF4 L 301 " - pdb=" SG CYS L 173 " pdb=" SF4 N 301 " pdb="FE2 SF4 N 301 " - pdb=" SG CYS N 205 " pdb="FE3 SF4 N 301 " - pdb=" SG CYS N 173 " pdb="FE1 SF4 N 301 " - pdb=" SG CYS N 182 " pdb="FE4 SF4 N 301 " - pdb=" SG CYS N 212 " pdb=" SF4 f 301 " pdb="FE2 SF4 f 301 " - pdb=" SG CYS f 205 " pdb="FE3 SF4 f 301 " - pdb=" SG CYS f 173 " pdb="FE1 SF4 f 301 " - pdb=" SG CYS f 182 " pdb="FE4 SF4 f 301 " - pdb=" SG CYS f 212 " Number of angles added : 36 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6086 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 15.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'E' and resid 54 through 66 removed outlier: 3.701A pdb=" N LEU E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.528A pdb=" N VAL F 45 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 227 No H-bonds generated for 'chain 'F' and resid 225 through 227' Processing helix chain 'F' and resid 271 through 282 Processing helix chain 'F' and resid 297 through 310 Processing helix chain 'F' and resid 334 through 346 removed outlier: 3.610A pdb=" N MET F 346 " --> pdb=" O PHE F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 395 removed outlier: 3.515A pdb=" N ARG F 395 " --> pdb=" O LEU F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 427 removed outlier: 3.958A pdb=" N ARG F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 458 Processing helix chain 'F' and resid 467 through 473 removed outlier: 3.636A pdb=" N LEU F 471 " --> pdb=" O ALA F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 488 Processing helix chain 'F' and resid 594 through 601 Processing helix chain 'J' and resid 40 through 43 removed outlier: 4.092A pdb=" N LYS J 43 " --> pdb=" O ASP J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 43' Processing helix chain 'J' and resid 271 through 281 Processing helix chain 'J' and resid 297 through 309 Processing helix chain 'J' and resid 334 through 346 Processing helix chain 'J' and resid 391 through 395 Processing helix chain 'J' and resid 419 through 424 Processing helix chain 'J' and resid 440 through 458 Processing helix chain 'J' and resid 467 through 473 removed outlier: 3.834A pdb=" N LEU J 471 " --> pdb=" O ALA J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 483 through 488 Processing helix chain 'J' and resid 594 through 600 Processing helix chain 'K' and resid 54 through 64 Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.585A pdb=" N ALA L 92 " --> pdb=" O VAL L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'L' and resid 208 through 215 removed outlier: 3.881A pdb=" N ARG L 215 " --> pdb=" O GLY L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 221 removed outlier: 4.495A pdb=" N GLY L 219 " --> pdb=" O ASN L 216 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE L 221 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 66 removed outlier: 4.323A pdb=" N THR M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU M 58 " --> pdb=" O GLU M 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 29 through 32 Processing helix chain 'N' and resid 86 through 93 removed outlier: 4.185A pdb=" N ALA N 92 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 114 through 118 Processing helix chain 'N' and resid 208 through 215 Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'Y' and resid 54 through 66 removed outlier: 4.192A pdb=" N LEU Y 58 " --> pdb=" O GLU Y 54 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS Y 65 " --> pdb=" O PHE Y 61 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY Y 66 " --> pdb=" O LEU Y 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 45 Processing helix chain 'Z' and resid 271 through 281 Processing helix chain 'Z' and resid 297 through 309 Processing helix chain 'Z' and resid 334 through 346 Processing helix chain 'Z' and resid 391 through 395 Processing helix chain 'Z' and resid 419 through 426 removed outlier: 3.681A pdb=" N ARG Z 425 " --> pdb=" O GLN Z 421 " (cutoff:3.500A) Processing helix chain 'Z' and resid 440 through 458 Processing helix chain 'Z' and resid 467 through 472 removed outlier: 3.848A pdb=" N LEU Z 471 " --> pdb=" O ALA Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 487 Processing helix chain 'Z' and resid 595 through 602 removed outlier: 3.532A pdb=" N GLY Z 602 " --> pdb=" O ILE Z 598 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 66 removed outlier: 3.744A pdb=" N HIS e 65 " --> pdb=" O PHE e 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 13 removed outlier: 4.049A pdb=" N THR f 13 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 32 removed outlier: 3.523A pdb=" N GLY f 32 " --> pdb=" O THR f 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 29 through 32' Processing helix chain 'f' and resid 83 through 87 removed outlier: 4.276A pdb=" N MET f 87 " --> pdb=" O LEU f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 92 removed outlier: 3.826A pdb=" N ALA f 92 " --> pdb=" O THR f 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 94 through 99 removed outlier: 3.571A pdb=" N VAL f 99 " --> pdb=" O GLN f 96 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 113 No H-bonds generated for 'chain 'f' and resid 111 through 113' Processing helix chain 'f' and resid 114 through 118 Processing helix chain 'f' and resid 199 through 203 removed outlier: 3.794A pdb=" N ASP f 203 " --> pdb=" O ILE f 200 " (cutoff:3.500A) Processing helix chain 'f' and resid 208 through 216 Processing helix chain 'f' and resid 217 through 221 removed outlier: 3.674A pdb=" N PHE f 221 " --> pdb=" O VAL f 218 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 66 removed outlier: 4.077A pdb=" N THR m 56 " --> pdb=" O ARG m 52 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL m 57 " --> pdb=" O GLU m 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.732A pdb=" N ASP E 13 " --> pdb=" O SER E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 51 current: chain 'E' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 82 through 86 current: chain 'E' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 97 through 106 current: chain 'K' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 43 through 51 current: chain 'K' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 82 through 86 current: chain 'K' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 97 through 106 current: chain 'M' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 43 through 51 current: chain 'M' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 82 through 86 current: chain 'M' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 97 through 106 current: chain 'Y' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 43 through 51 current: chain 'Y' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 82 through 86 current: chain 'Y' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 97 through 106 current: chain 'e' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 43 through 51 current: chain 'e' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 82 through 86 current: chain 'e' and resid 97 through 106 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 97 through 106 current: chain 'm' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 43 through 51 current: chain 'm' and resid 82 through 86 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 82 through 86 current: chain 'm' and resid 97 through 106 Processing sheet with id=AA2, first strand: chain 'E' and resid 21 through 24 Processing sheet with id=AA3, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain 'F' and resid 35 through 38 removed outlier: 7.172A pdb=" N GLY F 240 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU F 238 " --> pdb=" O PRO F 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 85 through 94 removed outlier: 5.838A pdb=" N SER F 200 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR F 92 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU F 198 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR F 115 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR F 202 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG F 113 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU F 204 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG F 111 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 179 through 183 removed outlier: 6.337A pdb=" N ILE F 141 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR F 149 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'F' and resid 249 through 250 removed outlier: 3.554A pdb=" N GLN F 255 " --> pdb=" O ASN F 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'F' and resid 328 through 329 Processing sheet with id=AB3, first strand: chain 'F' and resid 350 through 353 Processing sheet with id=AB4, first strand: chain 'F' and resid 368 through 372 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 368 through 372 current: chain 'F' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 460 through 463 current: chain 'F' and resid 570 through 578 removed outlier: 6.865A pdb=" N THR F 587 " --> pdb=" O VAL F 574 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE F 576 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA F 585 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 411 through 418 removed outlier: 3.821A pdb=" N GLU F 411 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 493 through 499 removed outlier: 6.834A pdb=" N THR F 506 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL F 498 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR F 504 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS F 543 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL F 538 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS F 545 " --> pdb=" O GLN F 536 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL F 524 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL F 558 " --> pdb=" O VAL F 524 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 191 through 193 Processing sheet with id=AB8, first strand: chain 'I' and resid 202 through 207 removed outlier: 6.324A pdb=" N VAL I 202 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA J 29 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER I 204 " --> pdb=" O ILE J 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 218 through 221 removed outlier: 5.643A pdb=" N THR J 149 " --> pdb=" O ILE J 141 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE J 141 " --> pdb=" O THR J 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'J' and resid 86 through 94 removed outlier: 7.203A pdb=" N SER J 86 " --> pdb=" O ILE J 205 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE J 205 " --> pdb=" O SER J 86 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR J 88 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR J 203 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU J 90 " --> pdb=" O SER J 201 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER J 201 " --> pdb=" O LEU J 90 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR J 197 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR J 115 " --> pdb=" O SER J 200 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR J 202 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG J 113 " --> pdb=" O TYR J 202 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU J 204 " --> pdb=" O ARG J 111 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG J 111 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 249 through 250 Processing sheet with id=AC4, first strand: chain 'J' and resid 311 through 313 Processing sheet with id=AC5, first strand: chain 'J' and resid 348 through 352 Processing sheet with id=AC6, first strand: chain 'J' and resid 369 through 371 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 369 through 371 current: chain 'J' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 460 through 463 current: chain 'J' and resid 570 through 577 removed outlier: 6.939A pdb=" N THR J 587 " --> pdb=" O VAL J 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 411 through 418 removed outlier: 3.848A pdb=" N GLU J 411 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 492 through 494 removed outlier: 6.624A pdb=" N VAL J 558 " --> pdb=" O VAL J 524 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL J 524 " --> pdb=" O VAL J 558 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 537 " --> pdb=" O LYS J 545 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS J 543 " --> pdb=" O THR J 539 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 21 through 23 Processing sheet with id=AD1, first strand: chain 'L' and resid 49 through 51 removed outlier: 6.958A pdb=" N PHE L 37 " --> pdb=" O GLN L 57 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU L 138 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER L 153 " --> pdb=" O GLU L 138 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS L 140 " --> pdb=" O VAL L 151 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 151 " --> pdb=" O CYS L 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 21 through 24 Processing sheet with id=AD3, first strand: chain 'N' and resid 49 through 51 removed outlier: 10.314A pdb=" N GLN N 55 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE N 37 " --> pdb=" O GLN N 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 61 through 63 removed outlier: 6.690A pdb=" N SER N 147 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU N 143 " --> pdb=" O SER N 147 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER N 149 " --> pdb=" O SER N 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN N 139 " --> pdb=" O VAL N 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 21 through 24 Processing sheet with id=AD6, first strand: chain 'Z' and resid 64 through 69 removed outlier: 6.520A pdb=" N LEU Z 23 " --> pdb=" O ILE h 207 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE h 207 " --> pdb=" O LEU Z 23 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER Z 25 " --> pdb=" O GLN h 205 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN h 205 " --> pdb=" O SER Z 25 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE Z 27 " --> pdb=" O VAL h 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 84 through 94 removed outlier: 7.173A pdb=" N SER Z 86 " --> pdb=" O ILE Z 205 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE Z 205 " --> pdb=" O SER Z 86 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR Z 88 " --> pdb=" O THR Z 203 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR Z 203 " --> pdb=" O THR Z 88 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU Z 90 " --> pdb=" O SER Z 201 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER Z 201 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR Z 197 " --> pdb=" O VAL Z 94 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR Z 115 " --> pdb=" O SER Z 200 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR Z 202 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG Z 113 " --> pdb=" O TYR Z 202 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU Z 204 " --> pdb=" O ARG Z 111 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG Z 111 " --> pdb=" O GLU Z 204 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 179 through 183 removed outlier: 6.234A pdb=" N ILE Z 141 " --> pdb=" O THR Z 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR Z 149 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG Z 143 " --> pdb=" O TRP Z 147 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP Z 147 " --> pdb=" O ARG Z 143 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP Z 152 " --> pdb=" O ILE h 221 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE h 221 " --> pdb=" O ASP Z 152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 243 through 246 Processing sheet with id=AE1, first strand: chain 'Z' and resid 249 through 250 Processing sheet with id=AE2, first strand: chain 'Z' and resid 311 through 313 Processing sheet with id=AE3, first strand: chain 'Z' and resid 327 through 329 Processing sheet with id=AE4, first strand: chain 'Z' and resid 349 through 352 Processing sheet with id=AE5, first strand: chain 'Z' and resid 369 through 371 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 369 through 371 current: chain 'Z' and resid 460 through 463 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 460 through 463 current: chain 'Z' and resid 570 through 578 removed outlier: 6.987A pdb=" N THR Z 587 " --> pdb=" O VAL Z 574 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE Z 576 " --> pdb=" O ALA Z 585 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA Z 585 " --> pdb=" O ILE Z 576 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 411 through 418 removed outlier: 3.604A pdb=" N GLU Z 411 " --> pdb=" O ASP Z 405 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 492 through 499 removed outlier: 3.881A pdb=" N SER Z 537 " --> pdb=" O LYS Z 545 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 21 through 23 Processing sheet with id=AE9, first strand: chain 'f' and resid 49 through 51 removed outlier: 11.622A pdb=" N ARG f 35 " --> pdb=" O GLN f 55 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N GLN f 57 " --> pdb=" O ARG f 35 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE f 37 " --> pdb=" O GLN f 57 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL f 151 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N CYS f 140 " --> pdb=" O SER f 149 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER f 149 " --> pdb=" O CYS f 140 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1608 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: 8.72 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.41: 10936 1.41 - 1.67: 15337 1.67 - 1.93: 195 1.93 - 2.19: 6 2.19 - 2.45: 30 Bond restraints: 26504 Sorted by residual: bond pdb=" C PRO F 475 " pdb=" O PRO F 475 " ideal model delta sigma weight residual 1.233 1.154 0.079 1.21e-02 6.83e+03 4.24e+01 bond pdb=" C ALA F 293 " pdb=" O ALA F 293 " ideal model delta sigma weight residual 1.233 1.309 -0.077 1.21e-02 6.83e+03 4.00e+01 bond pdb=" C LEU F 357 " pdb=" O LEU F 357 " ideal model delta sigma weight residual 1.235 1.159 0.076 1.22e-02 6.72e+03 3.93e+01 bond pdb=" C ILE J 205 " pdb=" O ILE J 205 " ideal model delta sigma weight residual 1.238 1.170 0.067 1.10e-02 8.26e+03 3.73e+01 bond pdb=" C PRO N 77 " pdb=" O PRO N 77 " ideal model delta sigma weight residual 1.235 1.157 0.079 1.30e-02 5.92e+03 3.65e+01 ... (remaining 26499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 35093 4.64 - 9.29: 906 9.29 - 13.93: 21 13.93 - 18.57: 1 18.57 - 23.21: 1 Bond angle restraints: 36022 Sorted by residual: angle pdb=" C PHE J 177 " pdb=" CA PHE J 177 " pdb=" CB PHE J 177 " ideal model delta sigma weight residual 110.42 87.21 23.21 1.99e+00 2.53e-01 1.36e+02 angle pdb=" CA TYR F 268 " pdb=" C TYR F 268 " pdb=" O TYR F 268 " ideal model delta sigma weight residual 120.69 110.12 10.57 1.14e+00 7.69e-01 8.60e+01 angle pdb=" CA TRP N 175 " pdb=" C TRP N 175 " pdb=" O TRP N 175 " ideal model delta sigma weight residual 121.44 112.22 9.22 1.08e+00 8.57e-01 7.29e+01 angle pdb=" CA ARG F 241 " pdb=" C ARG F 241 " pdb=" O ARG F 241 " ideal model delta sigma weight residual 121.87 112.57 9.30 1.10e+00 8.26e-01 7.15e+01 angle pdb=" C ASN J 235 " pdb=" CA ASN J 235 " pdb=" CB ASN J 235 " ideal model delta sigma weight residual 110.79 99.11 11.68 1.39e+00 5.18e-01 7.06e+01 ... (remaining 36017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13334 17.56 - 35.12: 1760 35.12 - 52.68: 557 52.68 - 70.24: 113 70.24 - 87.80: 37 Dihedral angle restraints: 15801 sinusoidal: 6313 harmonic: 9488 Sorted by residual: dihedral pdb=" CA PHE f 163 " pdb=" C PHE f 163 " pdb=" N PRO f 164 " pdb=" CA PRO f 164 " ideal model delta harmonic sigma weight residual -180.00 -99.50 -80.50 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA PHE L 163 " pdb=" C PHE L 163 " pdb=" N PRO L 164 " pdb=" CA PRO L 164 " ideal model delta harmonic sigma weight residual -180.00 -115.46 -64.54 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA ARG J 175 " pdb=" C ARG J 175 " pdb=" N PRO J 176 " pdb=" CA PRO J 176 " ideal model delta harmonic sigma weight residual 180.00 121.74 58.26 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 15798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2304 0.092 - 0.184: 1448 0.184 - 0.277: 213 0.277 - 0.369: 18 0.369 - 0.461: 3 Chirality restraints: 3986 Sorted by residual: chirality pdb="FE1 SF4 L 301 " pdb=" S2 SF4 L 301 " pdb=" S3 SF4 L 301 " pdb=" S4 SF4 L 301 " both_signs ideal model delta sigma weight residual False -10.55 -11.02 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA CYS F 348 " pdb=" N CYS F 348 " pdb=" C CYS F 348 " pdb=" CB CYS F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA PHE N 163 " pdb=" N PHE N 163 " pdb=" C PHE N 163 " pdb=" CB PHE N 163 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 3983 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 274 " -0.050 2.00e-02 2.50e+03 2.94e-02 2.17e+01 pdb=" CG TRP J 274 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP J 274 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 274 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP J 274 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 274 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP J 274 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 274 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 274 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP J 274 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Z 274 " 0.045 2.00e-02 2.50e+03 2.82e-02 1.98e+01 pdb=" CG TRP Z 274 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP Z 274 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP Z 274 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP Z 274 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP Z 274 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP Z 274 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP Z 274 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP Z 274 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Z 274 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 163 " -0.046 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE N 163 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE N 163 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE N 163 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE N 163 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE N 163 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE N 163 " -0.029 2.00e-02 2.50e+03 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 72 2.40 - 3.03: 15379 3.03 - 3.65: 36849 3.65 - 4.28: 58485 4.28 - 4.90: 97468 Nonbonded interactions: 208253 Sorted by model distance: nonbonded pdb=" O THR J 105 " pdb=" OG1 THR J 105 " model vdw 1.777 3.040 nonbonded pdb=" OG SER F 31 " pdb=" N GLU F 32 " model vdw 1.895 3.120 nonbonded pdb=" OG SER Z 224 " pdb=" O THR h 174 " model vdw 1.989 3.040 nonbonded pdb=" O ASP L 203 " pdb=" OD1 ASP L 203 " model vdw 2.082 3.040 nonbonded pdb=" O GLU Z 32 " pdb=" O GLY Z 33 " model vdw 2.095 3.040 ... (remaining 208248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'Y' selection = chain 'e' selection = chain 'm' } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 11 through 604) selection = (chain 'Z' and resid 11 through 604) } ncs_group { reference = chain 'I' selection = (chain 'P' and resid 167 through 222) selection = (chain 'h' and resid 167 through 222) } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 60.120 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.016 0.508 26519 Z= 1.125 Angle : 2.043 42.342 36064 Z= 1.402 Chirality : 0.105 0.461 3986 Planarity : 0.007 0.070 4690 Dihedral : 18.167 87.803 9706 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 2.71 % Allowed : 13.56 % Favored : 83.73 % Rotamer: Outliers : 8.53 % Allowed : 21.19 % Favored : 70.28 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.12), residues: 3282 helix: -1.91 (0.22), residues: 381 sheet: -1.94 (0.16), residues: 894 loop : -3.11 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.006 TRP J 274 HIS 0.019 0.004 HIS J 396 PHE 0.055 0.007 PHE J 177 TYR 0.051 0.007 TYR F 328 ARG 0.013 0.001 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.19701 ( 626) hydrogen bonds : angle 7.97735 ( 1608) metal coordination : bond 0.21139 ( 12) metal coordination : angle 14.55571 ( 36) SS BOND : bond 0.09257 ( 3) SS BOND : angle 6.08565 ( 6) covalent geometry : bond 0.01525 (26504) covalent geometry : angle 1.99057 (36022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 380 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8782 (tm-30) REVERT: E 78 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8669 (mt-10) REVERT: E 99 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7777 (mm-30) REVERT: F 17 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (p0) REVERT: F 144 ASN cc_start: 0.9370 (t0) cc_final: 0.8400 (m110) REVERT: F 162 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8610 (tp40) REVERT: F 221 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: F 261 ASP cc_start: 0.9624 (OUTLIER) cc_final: 0.9187 (p0) REVERT: F 489 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7768 (tt) REVERT: F 496 LEU cc_start: 0.8000 (mt) cc_final: 0.7638 (mt) REVERT: I 171 LYS cc_start: 0.5495 (OUTLIER) cc_final: 0.5185 (tptm) REVERT: I 172 GLN cc_start: 0.7009 (tp-100) cc_final: 0.6627 (tp40) REVERT: J 32 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: J 47 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8564 (mt) REVERT: J 134 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7961 (tm-30) REVERT: J 175 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8033 (mtm-85) REVERT: J 187 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7441 (t70) REVERT: J 272 MET cc_start: 0.8987 (ttm) cc_final: 0.8594 (ttt) REVERT: J 483 ASP cc_start: 0.8637 (t70) cc_final: 0.8351 (t0) REVERT: J 523 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (mt) REVERT: J 568 GLN cc_start: 0.7536 (tp40) cc_final: 0.7215 (tp40) REVERT: J 601 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6599 (m110) REVERT: K 9 LYS cc_start: 0.7809 (mmtp) cc_final: 0.7309 (mmtp) REVERT: K 31 GLN cc_start: 0.8879 (mt0) cc_final: 0.8050 (mt0) REVERT: K 40 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.7017 (t0) REVERT: K 63 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8130 (mm-30) REVERT: K 64 GLU cc_start: 0.8877 (mp0) cc_final: 0.8417 (mp0) REVERT: K 97 ARG cc_start: 0.7241 (mmp-170) cc_final: 0.6517 (mmp-170) REVERT: L 1 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7905 (mmm) REVERT: L 59 TYR cc_start: 0.9202 (t80) cc_final: 0.8855 (t80) REVERT: L 69 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8854 (m-40) REVERT: M 9 LYS cc_start: 0.2275 (OUTLIER) cc_final: 0.0769 (mmmm) REVERT: M 52 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7881 (mtp-110) REVERT: M 63 GLU cc_start: 0.8281 (tp30) cc_final: 0.8045 (tp30) REVERT: M 79 TRP cc_start: 0.8075 (m100) cc_final: 0.7788 (m100) REVERT: P 180 ASP cc_start: 0.8942 (t0) cc_final: 0.8672 (t0) REVERT: Y 2 LYS cc_start: 0.6322 (tptt) cc_final: 0.6027 (tptp) REVERT: Y 24 ARG cc_start: 0.9343 (ttp-110) cc_final: 0.8954 (ttp80) REVERT: Y 40 ASN cc_start: 0.7577 (p0) cc_final: 0.7308 (p0) REVERT: Y 63 GLU cc_start: 0.8666 (pp20) cc_final: 0.8406 (pp20) REVERT: Y 69 LYS cc_start: 0.7857 (tmtt) cc_final: 0.7266 (tmtt) REVERT: Y 72 LEU cc_start: 0.8995 (mp) cc_final: 0.8771 (mp) REVERT: Z 346 MET cc_start: 0.9385 (ptm) cc_final: 0.9177 (ptt) REVERT: Z 425 ARG cc_start: 0.9181 (ptt-90) cc_final: 0.8821 (ptm160) REVERT: e 12 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7484 (ttt) REVERT: e 95 MET cc_start: 0.7282 (tpp) cc_final: 0.6785 (tpp) REVERT: e 103 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8536 (mm-30) REVERT: f 2 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: f 111 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7877 (ptp-170) REVERT: f 149 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.9027 (p) REVERT: f 213 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8530 (mtpp) REVERT: h 182 MET cc_start: 0.9150 (mmm) cc_final: 0.8832 (mmm) REVERT: h 196 MET cc_start: 0.9060 (tpp) cc_final: 0.8689 (tpp) REVERT: m 9 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7499 (mtmm) REVERT: m 59 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7697 (tm-30) outliers start: 244 outliers final: 126 residues processed: 579 average time/residue: 0.4375 time to fit residues: 384.4753 Evaluate side-chains 475 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 328 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 162 GLN Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 211 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 599 VAL Chi-restraints excluded: chain F residue 604 HIS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain J residue 280 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 407 ASN Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 463 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 601 ASN Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 103 THR Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 181 MET Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 215 THR Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 248 ASN Chi-restraints excluded: chain Z residue 339 LEU Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 461 THR Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 12 MET Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain f residue 2 GLN Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 111 ARG Chi-restraints excluded: chain f residue 149 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 213 LYS Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 181 ASN Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 205 GLN Chi-restraints excluded: chain h residue 214 ASP Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 129 optimal weight: 0.0770 chunk 251 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 250 ASN F 443 GLN F 460 GLN I 172 GLN I 185 GLN I 205 GLN J 22 GLN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 GLN K 65 HIS L 2 GLN M 31 GLN N 6 GLN N 42 GLN Z 22 GLN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 332 GLN e 40 ASN e 106 GLN f 6 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096406 restraints weight = 46742.489| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.79 r_work: 0.3006 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26519 Z= 0.147 Angle : 0.758 23.321 36064 Z= 0.376 Chirality : 0.047 0.205 3986 Planarity : 0.005 0.094 4690 Dihedral : 9.277 81.082 3858 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 1.01 % Allowed : 9.32 % Favored : 89.67 % Rotamer: Outliers : 5.21 % Allowed : 23.22 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.66 (0.14), residues: 3282 helix: 0.05 (0.26), residues: 382 sheet: -1.41 (0.16), residues: 1024 loop : -2.46 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 89 HIS 0.006 0.001 HIS F 445 PHE 0.021 0.001 PHE N 163 TYR 0.020 0.001 TYR Z 212 ARG 0.006 0.001 ARG e 5 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 626) hydrogen bonds : angle 5.75475 ( 1608) metal coordination : bond 0.00609 ( 12) metal coordination : angle 8.70767 ( 36) SS BOND : bond 0.00493 ( 3) SS BOND : angle 3.00815 ( 6) covalent geometry : bond 0.00315 (26504) covalent geometry : angle 0.70515 (36022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 368 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8490 (mt-10) REVERT: F 72 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8331 (mm-30) REVERT: F 144 ASN cc_start: 0.8993 (t0) cc_final: 0.8421 (m110) REVERT: F 182 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8070 (ptm160) REVERT: F 264 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: F 287 MET cc_start: 0.9139 (tpp) cc_final: 0.8796 (tpp) REVERT: F 489 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7470 (tt) REVERT: F 516 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7676 (p) REVERT: J 22 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: J 27 ILE cc_start: 0.9192 (mt) cc_final: 0.8878 (tt) REVERT: J 28 ASP cc_start: 0.8267 (m-30) cc_final: 0.7933 (m-30) REVERT: J 96 TYR cc_start: 0.7408 (t80) cc_final: 0.7048 (t80) REVERT: J 134 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7429 (tm-30) REVERT: J 503 ARG cc_start: 0.7886 (ptt-90) cc_final: 0.7470 (ptt-90) REVERT: K 9 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7678 (mmtp) REVERT: K 22 LYS cc_start: 0.9008 (ttpp) cc_final: 0.8786 (ptmt) REVERT: K 31 GLN cc_start: 0.8704 (mt0) cc_final: 0.8159 (mt0) REVERT: K 64 GLU cc_start: 0.8433 (mp0) cc_final: 0.8144 (pt0) REVERT: L 1 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7452 (tpt) REVERT: L 59 TYR cc_start: 0.8678 (t80) cc_final: 0.8270 (t80) REVERT: L 69 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8130 (m-40) REVERT: L 214 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8145 (t80) REVERT: M 13 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8034 (t0) REVERT: M 27 ASP cc_start: 0.7990 (p0) cc_final: 0.7662 (p0) REVERT: M 58 LEU cc_start: 0.8532 (tp) cc_final: 0.8322 (tp) REVERT: M 64 GLU cc_start: 0.8975 (tp30) cc_final: 0.8418 (tm-30) REVERT: N 3 ASP cc_start: 0.7746 (p0) cc_final: 0.7502 (p0) REVERT: P 172 GLN cc_start: 0.7182 (mp10) cc_final: 0.6677 (tp40) REVERT: P 180 ASP cc_start: 0.8678 (t0) cc_final: 0.8324 (t0) REVERT: Y 24 ARG cc_start: 0.9214 (ttp-110) cc_final: 0.8894 (ttp80) REVERT: Y 27 ASP cc_start: 0.8288 (m-30) cc_final: 0.8073 (m-30) REVERT: Y 69 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7738 (tmtt) REVERT: Z 179 ILE cc_start: 0.9130 (pp) cc_final: 0.8586 (pt) REVERT: Z 272 MET cc_start: 0.9018 (tpp) cc_final: 0.8736 (tpt) REVERT: e 12 MET cc_start: 0.7874 (ttt) cc_final: 0.7396 (ttt) REVERT: e 59 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: e 95 MET cc_start: 0.7253 (tpp) cc_final: 0.6956 (tpp) REVERT: f 159 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8514 (m-30) REVERT: h 171 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7517 (mptt) REVERT: h 182 MET cc_start: 0.8495 (mmm) cc_final: 0.8110 (mmm) REVERT: m 5 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6566 (mtm110) REVERT: m 59 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7403 (tm-30) outliers start: 149 outliers final: 82 residues processed: 483 average time/residue: 0.4115 time to fit residues: 305.4962 Evaluate side-chains 430 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 336 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 211 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 604 HIS Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 280 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 215 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 213 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 253 optimal weight: 0.0970 chunk 124 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 256 optimal weight: 0.8980 chunk 247 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 GLN I 187 ASN J 22 GLN J 162 GLN L 69 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 195 ASN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 228 ASN h 172 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095592 restraints weight = 46483.818| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.82 r_work: 0.2980 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26519 Z= 0.173 Angle : 0.708 19.719 36064 Z= 0.350 Chirality : 0.047 0.179 3986 Planarity : 0.005 0.083 4690 Dihedral : 7.219 69.465 3697 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 1.04 % Allowed : 10.79 % Favored : 88.18 % Rotamer: Outliers : 4.79 % Allowed : 24.27 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.14), residues: 3282 helix: 0.55 (0.27), residues: 376 sheet: -1.20 (0.16), residues: 1057 loop : -2.31 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 89 HIS 0.004 0.001 HIS J 282 PHE 0.014 0.001 PHE F 68 TYR 0.014 0.001 TYR Z 212 ARG 0.007 0.000 ARG e 5 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 626) hydrogen bonds : angle 5.37366 ( 1608) metal coordination : bond 0.01236 ( 12) metal coordination : angle 7.80045 ( 36) SS BOND : bond 0.00415 ( 3) SS BOND : angle 4.26803 ( 6) covalent geometry : bond 0.00402 (26504) covalent geometry : angle 0.66220 (36022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 351 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 78 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8429 (mt-10) REVERT: F 169 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7878 (ptp) REVERT: F 264 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: F 489 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7539 (tt) REVERT: F 516 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7702 (p) REVERT: J 16 ASP cc_start: 0.7353 (t0) cc_final: 0.6961 (t0) REVERT: J 27 ILE cc_start: 0.9151 (mt) cc_final: 0.8850 (tt) REVERT: J 28 ASP cc_start: 0.8348 (m-30) cc_final: 0.7998 (m-30) REVERT: J 96 TYR cc_start: 0.7461 (t80) cc_final: 0.7017 (t80) REVERT: J 134 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7535 (tm-30) REVERT: J 183 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6682 (ttt180) REVERT: J 503 ARG cc_start: 0.7918 (ptt-90) cc_final: 0.7449 (ptt-90) REVERT: J 523 LEU cc_start: 0.8596 (mm) cc_final: 0.8356 (mm) REVERT: K 9 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7448 (mmtp) REVERT: K 31 GLN cc_start: 0.8723 (mt0) cc_final: 0.8232 (mt0) REVERT: K 63 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7718 (mt-10) REVERT: K 64 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7976 (mp0) REVERT: K 97 ARG cc_start: 0.7216 (mmp-170) cc_final: 0.6558 (mmp-170) REVERT: L 59 TYR cc_start: 0.8668 (t80) cc_final: 0.8297 (t80) REVERT: L 71 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8782 (mmtt) REVERT: M 13 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8034 (t0) REVERT: M 64 GLU cc_start: 0.8946 (tp30) cc_final: 0.8410 (tm-30) REVERT: N 3 ASP cc_start: 0.7785 (p0) cc_final: 0.7526 (p0) REVERT: P 172 GLN cc_start: 0.7149 (mp10) cc_final: 0.6650 (tp40) REVERT: P 180 ASP cc_start: 0.8701 (t0) cc_final: 0.8367 (t0) REVERT: Y 69 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7643 (tmtt) REVERT: Z 179 ILE cc_start: 0.9230 (pp) cc_final: 0.8746 (pt) REVERT: Z 272 MET cc_start: 0.9128 (tpp) cc_final: 0.8843 (tpt) REVERT: e 12 MET cc_start: 0.7885 (ttt) cc_final: 0.7413 (ttt) REVERT: e 22 LYS cc_start: 0.8215 (tptt) cc_final: 0.7675 (tptt) REVERT: e 95 MET cc_start: 0.7289 (tpp) cc_final: 0.6954 (tpp) REVERT: f 159 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: h 171 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7647 (mptt) REVERT: h 197 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8225 (ptp90) REVERT: m 5 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6637 (mtm110) REVERT: m 9 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7368 (mtmm) REVERT: m 59 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7582 (tm-30) outliers start: 137 outliers final: 84 residues processed: 458 average time/residue: 0.4199 time to fit residues: 297.0193 Evaluate side-chains 416 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 323 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 228 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 291 optimal weight: 0.0670 chunk 300 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 269 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN K 40 ASN M 40 ASN Y 40 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 38 ASN e 106 GLN ** m 65 HIS ** 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 = 0.3681 r_free = 0.3681 target = 0.126417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099132 restraints weight = 46340.172| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.86 r_work: 0.3041 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26519 Z= 0.131 Angle : 0.669 16.312 36064 Z= 0.330 Chirality : 0.045 0.158 3986 Planarity : 0.005 0.086 4690 Dihedral : 6.366 66.038 3658 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.38 % Favored : 89.70 % Rotamer: Outliers : 4.34 % Allowed : 24.97 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.15 (0.15), residues: 3282 helix: 0.75 (0.28), residues: 376 sheet: -1.08 (0.16), residues: 1058 loop : -2.17 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 89 HIS 0.003 0.001 HIS e 65 PHE 0.012 0.001 PHE F 264 TYR 0.016 0.001 TYR Z 212 ARG 0.007 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 626) hydrogen bonds : angle 5.14540 ( 1608) metal coordination : bond 0.00889 ( 12) metal coordination : angle 7.16294 ( 36) SS BOND : bond 0.00641 ( 3) SS BOND : angle 3.18737 ( 6) covalent geometry : bond 0.00295 (26504) covalent geometry : angle 0.62863 (36022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 346 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8737 (tm-30) REVERT: E 78 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8348 (mt-10) REVERT: F 264 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: F 489 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7561 (tt) REVERT: F 516 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7653 (p) REVERT: I 221 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7023 (mt) REVERT: J 16 ASP cc_start: 0.7318 (t0) cc_final: 0.7096 (t0) REVERT: J 27 ILE cc_start: 0.9222 (mt) cc_final: 0.8879 (tt) REVERT: J 28 ASP cc_start: 0.8377 (m-30) cc_final: 0.7987 (m-30) REVERT: J 96 TYR cc_start: 0.7569 (t80) cc_final: 0.7147 (t80) REVERT: J 503 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.7444 (ptt-90) REVERT: J 600 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6934 (p0) REVERT: K 9 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7437 (mmtp) REVERT: K 54 GLU cc_start: 0.8586 (tt0) cc_final: 0.8248 (tm-30) REVERT: K 64 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7891 (mp0) REVERT: K 97 ARG cc_start: 0.7292 (mmp-170) cc_final: 0.6481 (mmp-170) REVERT: L 59 TYR cc_start: 0.8625 (t80) cc_final: 0.8260 (t80) REVERT: L 214 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8159 (t80) REVERT: M 13 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7879 (t0) REVERT: M 27 ASP cc_start: 0.8113 (p0) cc_final: 0.7779 (p0) REVERT: M 64 GLU cc_start: 0.8908 (tp30) cc_final: 0.8345 (tm-30) REVERT: N 3 ASP cc_start: 0.7774 (p0) cc_final: 0.7495 (p0) REVERT: N 95 MET cc_start: 0.8527 (mmp) cc_final: 0.8275 (mmp) REVERT: P 172 GLN cc_start: 0.7141 (mp10) cc_final: 0.6674 (tp40) REVERT: P 180 ASP cc_start: 0.8777 (t0) cc_final: 0.8425 (t0) REVERT: Y 69 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7639 (tmtt) REVERT: Z 36 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: Z 62 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7772 (p) REVERT: Z 179 ILE cc_start: 0.9221 (pp) cc_final: 0.8755 (pt) REVERT: e 12 MET cc_start: 0.7836 (ttt) cc_final: 0.7481 (ttt) REVERT: e 22 LYS cc_start: 0.8184 (tptt) cc_final: 0.7658 (tptp) REVERT: e 95 MET cc_start: 0.6920 (tpp) cc_final: 0.6597 (tpp) REVERT: h 171 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7610 (mptt) REVERT: h 197 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8199 (ptp90) REVERT: m 5 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6639 (mtm110) REVERT: m 59 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7488 (tm-30) outliers start: 124 outliers final: 86 residues processed: 441 average time/residue: 0.3953 time to fit residues: 268.4055 Evaluate side-chains 424 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 327 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 40 ASN Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 316 optimal weight: 10.0000 chunk 312 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 296 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 chunk 291 optimal weight: 0.3980 chunk 160 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097377 restraints weight = 46623.652| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.83 r_work: 0.3012 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26519 Z= 0.194 Angle : 0.689 17.551 36064 Z= 0.339 Chirality : 0.046 0.199 3986 Planarity : 0.005 0.082 4690 Dihedral : 6.287 65.775 3647 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.66 % Favored : 88.36 % Rotamer: Outliers : 5.38 % Allowed : 24.44 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.14 (0.15), residues: 3282 helix: 0.72 (0.28), residues: 376 sheet: -1.06 (0.16), residues: 1054 loop : -2.17 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 89 HIS 0.005 0.001 HIS J 282 PHE 0.014 0.001 PHE Z 68 TYR 0.014 0.001 TYR m 77 ARG 0.008 0.000 ARG e 5 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 626) hydrogen bonds : angle 5.13543 ( 1608) metal coordination : bond 0.01485 ( 12) metal coordination : angle 7.40381 ( 36) SS BOND : bond 0.00752 ( 3) SS BOND : angle 3.11858 ( 6) covalent geometry : bond 0.00456 (26504) covalent geometry : angle 0.64725 (36022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 335 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8074 (ptm160) REVERT: F 264 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: F 489 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7626 (tt) REVERT: F 516 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7958 (p) REVERT: I 221 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6896 (mt) REVERT: J 16 ASP cc_start: 0.7358 (t0) cc_final: 0.7125 (t0) REVERT: J 27 ILE cc_start: 0.9212 (mt) cc_final: 0.8872 (tt) REVERT: J 28 ASP cc_start: 0.8430 (m-30) cc_final: 0.8030 (m-30) REVERT: J 96 TYR cc_start: 0.7466 (t80) cc_final: 0.6986 (t80) REVERT: J 183 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6430 (ttt180) REVERT: J 503 ARG cc_start: 0.7982 (ptt-90) cc_final: 0.7563 (ptt-90) REVERT: J 523 LEU cc_start: 0.8660 (mm) cc_final: 0.8277 (mt) REVERT: J 600 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7008 (p0) REVERT: K 9 LYS cc_start: 0.7731 (mmtp) cc_final: 0.7315 (mmtp) REVERT: K 31 GLN cc_start: 0.8734 (mt0) cc_final: 0.8077 (mt0) REVERT: K 54 GLU cc_start: 0.8636 (tt0) cc_final: 0.8017 (tm-30) REVERT: K 97 ARG cc_start: 0.7414 (mmp-170) cc_final: 0.7159 (mmp-170) REVERT: L 59 TYR cc_start: 0.8642 (t80) cc_final: 0.8296 (t80) REVERT: L 214 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8168 (t80) REVERT: M 27 ASP cc_start: 0.8036 (p0) cc_final: 0.7701 (p0) REVERT: M 64 GLU cc_start: 0.8903 (tp30) cc_final: 0.8312 (tm-30) REVERT: N 3 ASP cc_start: 0.7795 (p0) cc_final: 0.7518 (p0) REVERT: P 172 GLN cc_start: 0.7244 (mp10) cc_final: 0.6672 (tp40) REVERT: P 180 ASP cc_start: 0.8757 (t0) cc_final: 0.8372 (t0) REVERT: Y 69 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7643 (tmtt) REVERT: Z 36 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: Z 62 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7821 (p) REVERT: Z 179 ILE cc_start: 0.9257 (pp) cc_final: 0.8826 (pt) REVERT: Z 272 MET cc_start: 0.9151 (tpp) cc_final: 0.8867 (tpt) REVERT: e 12 MET cc_start: 0.7884 (ttt) cc_final: 0.7531 (ttt) REVERT: e 22 LYS cc_start: 0.8180 (tptt) cc_final: 0.7675 (tptp) REVERT: e 59 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: e 95 MET cc_start: 0.6859 (tpp) cc_final: 0.6511 (tpp) REVERT: f 159 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: h 171 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7592 (mptt) REVERT: h 197 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8237 (ptp90) REVERT: m 5 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6726 (mtm110) REVERT: m 52 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7879 (tpp80) REVERT: m 59 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7638 (tm-30) outliers start: 154 outliers final: 104 residues processed: 457 average time/residue: 0.4027 time to fit residues: 281.7537 Evaluate side-chains 446 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 327 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 50 VAL Chi-restraints excluded: chain m residue 52 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 174 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 320 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 ASN K 40 ASN L 2 GLN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 205 GLN ** m 65 HIS ** 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 = 0.3656 r_free = 0.3656 target = 0.124592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097261 restraints weight = 46437.961| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.63 r_work: 0.3025 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26519 Z= 0.193 Angle : 0.694 19.278 36064 Z= 0.339 Chirality : 0.046 0.190 3986 Planarity : 0.005 0.082 4690 Dihedral : 6.276 64.998 3642 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.27 % Favored : 88.76 % Rotamer: Outliers : 5.63 % Allowed : 24.51 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.15 (0.15), residues: 3282 helix: 0.78 (0.28), residues: 371 sheet: -1.06 (0.16), residues: 1041 loop : -2.18 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 89 HIS 0.004 0.001 HIS J 282 PHE 0.014 0.001 PHE F 264 TYR 0.015 0.001 TYR Z 212 ARG 0.007 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 626) hydrogen bonds : angle 5.14891 ( 1608) metal coordination : bond 0.01532 ( 12) metal coordination : angle 7.87125 ( 36) SS BOND : bond 0.00755 ( 3) SS BOND : angle 3.30470 ( 6) covalent geometry : bond 0.00454 (26504) covalent geometry : angle 0.64664 (36022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 330 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8813 (tm-30) REVERT: E 99 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7430 (mm-30) REVERT: F 182 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8128 (ptm160) REVERT: F 264 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: F 426 TYR cc_start: 0.7835 (m-10) cc_final: 0.7588 (m-10) REVERT: F 489 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7782 (tt) REVERT: F 516 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7961 (p) REVERT: F 563 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8105 (mm) REVERT: I 221 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6732 (mt) REVERT: J 16 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7208 (t0) REVERT: J 183 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6377 (ttt180) REVERT: J 344 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8275 (m) REVERT: J 503 ARG cc_start: 0.8078 (ptt-90) cc_final: 0.7670 (ptt-90) REVERT: J 523 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8238 (mt) REVERT: J 600 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6964 (p0) REVERT: K 9 LYS cc_start: 0.7643 (mmtp) cc_final: 0.7222 (mmtp) REVERT: K 54 GLU cc_start: 0.8624 (tt0) cc_final: 0.8003 (tm-30) REVERT: K 97 ARG cc_start: 0.7527 (mmp-170) cc_final: 0.6751 (mmp-170) REVERT: L 1 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7751 (tmm) REVERT: L 59 TYR cc_start: 0.8610 (t80) cc_final: 0.8213 (t80) REVERT: L 214 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8156 (t80) REVERT: M 27 ASP cc_start: 0.8022 (p0) cc_final: 0.7731 (p0) REVERT: M 64 GLU cc_start: 0.8887 (tp30) cc_final: 0.8304 (tm-30) REVERT: N 3 ASP cc_start: 0.7764 (p0) cc_final: 0.7485 (p0) REVERT: P 172 GLN cc_start: 0.7276 (mp10) cc_final: 0.6656 (tp40) REVERT: P 180 ASP cc_start: 0.8728 (t0) cc_final: 0.8363 (t0) REVERT: Y 27 ASP cc_start: 0.8484 (m-30) cc_final: 0.8234 (t0) REVERT: Y 69 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7607 (tmtt) REVERT: Y 78 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6685 (mm-30) REVERT: Y 80 ARG cc_start: 0.6828 (mtm-85) cc_final: 0.6527 (ptp-170) REVERT: Z 36 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: Z 62 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7845 (p) REVERT: Z 179 ILE cc_start: 0.9192 (pp) cc_final: 0.8776 (pt) REVERT: Z 272 MET cc_start: 0.9127 (tpp) cc_final: 0.8831 (tpt) REVERT: e 12 MET cc_start: 0.7956 (ttt) cc_final: 0.7606 (ttt) REVERT: e 59 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: e 95 MET cc_start: 0.6911 (tpp) cc_final: 0.6542 (tpp) REVERT: f 159 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: h 171 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7577 (mptt) REVERT: h 197 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8215 (ptp90) REVERT: m 5 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6892 (mtm110) REVERT: m 59 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7610 (tm-30) outliers start: 161 outliers final: 110 residues processed: 455 average time/residue: 0.3957 time to fit residues: 276.8682 Evaluate side-chains 449 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 320 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 344 SER Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain Y residue 40 ASN Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 50 VAL Chi-restraints excluded: chain m residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 218 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 246 optimal weight: 0.8980 chunk 273 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN K 40 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098533 restraints weight = 46358.054| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.66 r_work: 0.3040 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26519 Z= 0.150 Angle : 0.671 17.228 36064 Z= 0.328 Chirality : 0.045 0.163 3986 Planarity : 0.005 0.082 4690 Dihedral : 6.137 63.243 3642 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.98 % Allowed : 9.72 % Favored : 89.31 % Rotamer: Outliers : 5.38 % Allowed : 25.03 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.08 (0.15), residues: 3282 helix: 0.82 (0.28), residues: 377 sheet: -1.02 (0.16), residues: 1044 loop : -2.13 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 89 HIS 0.004 0.001 HIS J 282 PHE 0.013 0.001 PHE F 264 TYR 0.016 0.001 TYR m 77 ARG 0.008 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 626) hydrogen bonds : angle 5.05049 ( 1608) metal coordination : bond 0.01126 ( 12) metal coordination : angle 7.42428 ( 36) SS BOND : bond 0.00734 ( 3) SS BOND : angle 2.63875 ( 6) covalent geometry : bond 0.00348 (26504) covalent geometry : angle 0.62775 (36022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 339 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8849 (tm-30) REVERT: E 99 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7517 (mm-30) REVERT: F 36 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: F 182 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8169 (ptm160) REVERT: F 426 TYR cc_start: 0.7834 (m-10) cc_final: 0.7570 (m-10) REVERT: F 489 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7815 (tt) REVERT: F 516 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7895 (p) REVERT: I 221 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6772 (mt) REVERT: J 16 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7125 (t0) REVERT: J 27 ILE cc_start: 0.9179 (mt) cc_final: 0.8884 (tt) REVERT: J 183 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6366 (ttt180) REVERT: J 503 ARG cc_start: 0.8093 (ptt-90) cc_final: 0.7722 (ptt-90) REVERT: J 523 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8224 (mt) REVERT: J 600 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6963 (p0) REVERT: K 9 LYS cc_start: 0.7641 (mmtp) cc_final: 0.7212 (mmtp) REVERT: K 31 GLN cc_start: 0.8625 (mt0) cc_final: 0.7930 (mt0) REVERT: K 54 GLU cc_start: 0.8597 (tt0) cc_final: 0.7985 (tm-30) REVERT: K 64 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8113 (mp0) REVERT: K 97 ARG cc_start: 0.7584 (mmp-170) cc_final: 0.6782 (mmp-170) REVERT: L 1 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7704 (tmm) REVERT: L 59 TYR cc_start: 0.8605 (t80) cc_final: 0.8285 (t80) REVERT: L 214 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8159 (t80) REVERT: M 13 ASP cc_start: 0.8352 (m-30) cc_final: 0.7874 (t0) REVERT: M 27 ASP cc_start: 0.8038 (p0) cc_final: 0.7714 (p0) REVERT: M 64 GLU cc_start: 0.8856 (tp30) cc_final: 0.8279 (tm-30) REVERT: N 3 ASP cc_start: 0.7702 (p0) cc_final: 0.7397 (p0) REVERT: P 172 GLN cc_start: 0.7242 (mp10) cc_final: 0.6634 (tp40) REVERT: P 180 ASP cc_start: 0.8737 (t0) cc_final: 0.8366 (t0) REVERT: Y 27 ASP cc_start: 0.8465 (m-30) cc_final: 0.8201 (t0) REVERT: Y 40 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7155 (p0) REVERT: Y 69 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7631 (tmtt) REVERT: Y 78 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6567 (mm-30) REVERT: Z 36 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: Z 62 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7960 (p) REVERT: Z 179 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8760 (pt) REVERT: Z 272 MET cc_start: 0.9064 (tpp) cc_final: 0.8796 (tpt) REVERT: e 12 MET cc_start: 0.7981 (ttt) cc_final: 0.7674 (ttt) REVERT: e 59 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: e 95 MET cc_start: 0.6811 (tpp) cc_final: 0.6459 (tpp) REVERT: f 73 THR cc_start: 0.8225 (t) cc_final: 0.7973 (t) REVERT: f 159 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8504 (m-30) REVERT: h 171 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7570 (mptt) REVERT: m 5 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6805 (mtm110) outliers start: 154 outliers final: 107 residues processed: 460 average time/residue: 0.5259 time to fit residues: 376.8956 Evaluate side-chains 452 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 327 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 518 THR Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain Y residue 40 ASN Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 462 VAL Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 261 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 280 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 285 optimal weight: 0.0870 chunk 199 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN M 38 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100048 restraints weight = 46120.258| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.73 r_work: 0.3067 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26519 Z= 0.127 Angle : 0.657 14.518 36064 Z= 0.323 Chirality : 0.045 0.202 3986 Planarity : 0.005 0.095 4690 Dihedral : 5.936 61.077 3638 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.45 % Favored : 89.73 % Rotamer: Outliers : 4.72 % Allowed : 25.63 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.00 (0.15), residues: 3282 helix: 0.92 (0.28), residues: 374 sheet: -0.95 (0.16), residues: 1038 loop : -2.10 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 6 HIS 0.003 0.001 HIS F 445 PHE 0.014 0.001 PHE F 264 TYR 0.015 0.001 TYR Z 212 ARG 0.008 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 626) hydrogen bonds : angle 5.00096 ( 1608) metal coordination : bond 0.00831 ( 12) metal coordination : angle 6.88805 ( 36) SS BOND : bond 0.00803 ( 3) SS BOND : angle 3.20645 ( 6) covalent geometry : bond 0.00290 (26504) covalent geometry : angle 0.61860 (36022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 346 time to evaluate : 4.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8852 (tm-30) REVERT: E 99 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7550 (mm-30) REVERT: F 36 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: F 182 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8054 (ptm160) REVERT: F 426 TYR cc_start: 0.7851 (m-10) cc_final: 0.7538 (m-10) REVERT: F 489 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7836 (tt) REVERT: F 516 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7945 (p) REVERT: J 16 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7087 (t0) REVERT: J 27 ILE cc_start: 0.9194 (mt) cc_final: 0.8881 (tt) REVERT: J 96 TYR cc_start: 0.7324 (t80) cc_final: 0.6847 (t80) REVERT: J 183 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6407 (ttt180) REVERT: J 503 ARG cc_start: 0.8075 (ptt-90) cc_final: 0.7703 (ptt-90) REVERT: J 523 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8205 (mt) REVERT: J 600 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6915 (p0) REVERT: K 9 LYS cc_start: 0.7590 (mmtp) cc_final: 0.7148 (mmtp) REVERT: K 31 GLN cc_start: 0.8582 (mt0) cc_final: 0.7903 (mt0) REVERT: K 54 GLU cc_start: 0.8627 (tt0) cc_final: 0.8027 (tm-30) REVERT: K 64 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8078 (mp0) REVERT: K 97 ARG cc_start: 0.7546 (mmp-170) cc_final: 0.6847 (mmp-170) REVERT: L 1 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7704 (tmm) REVERT: L 59 TYR cc_start: 0.8613 (t80) cc_final: 0.8288 (t80) REVERT: L 214 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8172 (t80) REVERT: M 1 MET cc_start: 0.7144 (mpp) cc_final: 0.6910 (pmm) REVERT: M 13 ASP cc_start: 0.8343 (m-30) cc_final: 0.7882 (t0) REVERT: M 27 ASP cc_start: 0.8093 (p0) cc_final: 0.7776 (p0) REVERT: M 64 GLU cc_start: 0.8825 (tp30) cc_final: 0.8155 (tm-30) REVERT: N 3 ASP cc_start: 0.7697 (p0) cc_final: 0.7400 (p0) REVERT: P 172 GLN cc_start: 0.7292 (mp10) cc_final: 0.6604 (tp40) REVERT: P 180 ASP cc_start: 0.8787 (t0) cc_final: 0.8412 (t0) REVERT: Y 69 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7623 (tmtt) REVERT: Y 80 ARG cc_start: 0.6613 (mtm-85) cc_final: 0.6232 (ptp-170) REVERT: Z 36 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: Z 62 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8019 (p) REVERT: Z 179 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8769 (pt) REVERT: Z 272 MET cc_start: 0.9056 (tpp) cc_final: 0.8798 (tpt) REVERT: e 12 MET cc_start: 0.7910 (ttt) cc_final: 0.7629 (ttt) REVERT: e 59 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: e 95 MET cc_start: 0.6871 (tpp) cc_final: 0.6505 (tpp) REVERT: f 159 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8486 (m-30) REVERT: h 171 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7464 (mptt) REVERT: h 197 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8230 (ptp-170) REVERT: m 5 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6765 (mtm110) outliers start: 135 outliers final: 100 residues processed: 450 average time/residue: 0.4568 time to fit residues: 321.2435 Evaluate side-chains 449 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 332 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 518 THR Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 185 GLN Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 462 VAL Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 289 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 chunk 239 optimal weight: 0.7980 chunk 301 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 6 GLN ** m 65 HIS ** 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 = 0.3653 r_free = 0.3653 target = 0.124370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097357 restraints weight = 46722.493| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.89 r_work: 0.3003 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 26519 Z= 0.234 Angle : 0.719 17.499 36064 Z= 0.352 Chirality : 0.047 0.200 3986 Planarity : 0.005 0.102 4690 Dihedral : 6.131 63.612 3634 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.79 % Allowed : 11.09 % Favored : 88.12 % Rotamer: Outliers : 5.07 % Allowed : 25.35 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.16 (0.15), residues: 3282 helix: 0.77 (0.28), residues: 376 sheet: -1.12 (0.16), residues: 1062 loop : -2.17 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 6 HIS 0.005 0.001 HIS J 282 PHE 0.020 0.002 PHE f 163 TYR 0.021 0.001 TYR Z 328 ARG 0.009 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 626) hydrogen bonds : angle 5.09397 ( 1608) metal coordination : bond 0.01914 ( 12) metal coordination : angle 7.61369 ( 36) SS BOND : bond 0.00945 ( 3) SS BOND : angle 3.68793 ( 6) covalent geometry : bond 0.00555 (26504) covalent geometry : angle 0.67666 (36022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 328 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7488 (mm-30) REVERT: F 36 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: F 182 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7988 (ptm160) REVERT: F 264 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: F 516 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8089 (p) REVERT: I 221 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6761 (mt) REVERT: J 16 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7211 (t0) REVERT: J 27 ILE cc_start: 0.9200 (mt) cc_final: 0.8871 (tt) REVERT: J 183 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6304 (ttt180) REVERT: J 503 ARG cc_start: 0.8101 (ptt-90) cc_final: 0.7720 (ptt-90) REVERT: J 523 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8228 (mt) REVERT: J 600 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.6960 (p0) REVERT: K 5 ARG cc_start: 0.7571 (mpp80) cc_final: 0.7342 (mpp80) REVERT: K 9 LYS cc_start: 0.7578 (mmtp) cc_final: 0.7119 (mmtp) REVERT: K 31 GLN cc_start: 0.8680 (mt0) cc_final: 0.8035 (mt0) REVERT: K 54 GLU cc_start: 0.8670 (tt0) cc_final: 0.8000 (tm-30) REVERT: K 64 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8091 (mp0) REVERT: K 97 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7201 (mmp-170) REVERT: L 1 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: L 59 TYR cc_start: 0.8652 (t80) cc_final: 0.8272 (t80) REVERT: M 13 ASP cc_start: 0.8364 (m-30) cc_final: 0.7996 (t0) REVERT: M 27 ASP cc_start: 0.8055 (p0) cc_final: 0.7773 (p0) REVERT: M 64 GLU cc_start: 0.8868 (tp30) cc_final: 0.8277 (tm-30) REVERT: N 3 ASP cc_start: 0.7815 (p0) cc_final: 0.7530 (p0) REVERT: P 172 GLN cc_start: 0.7436 (mp10) cc_final: 0.6631 (tp40) REVERT: P 180 ASP cc_start: 0.8816 (t0) cc_final: 0.8424 (t0) REVERT: Y 1 MET cc_start: 0.6088 (mmt) cc_final: 0.5887 (mmt) REVERT: Y 69 LYS cc_start: 0.8037 (tmtt) cc_final: 0.7595 (tmtt) REVERT: Y 78 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6597 (mm-30) REVERT: Z 36 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: Z 62 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8015 (p) REVERT: Z 119 GLN cc_start: 0.7565 (tp40) cc_final: 0.7320 (tp40) REVERT: Z 179 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8805 (pt) REVERT: Z 332 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8382 (tp40) REVERT: e 12 MET cc_start: 0.7843 (ttt) cc_final: 0.7588 (ttt) REVERT: e 95 MET cc_start: 0.6715 (tpp) cc_final: 0.6344 (tpp) REVERT: f 1 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8559 (tmm) REVERT: f 159 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: h 171 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7411 (mptt) REVERT: h 197 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8184 (ptp-170) REVERT: m 5 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6879 (mtm110) outliers start: 145 outliers final: 112 residues processed: 440 average time/residue: 0.4154 time to fit residues: 282.9078 Evaluate side-chains 451 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 321 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 518 THR Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 185 GLN Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 332 GLN Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 462 VAL Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 63 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 140 optimal weight: 0.0770 chunk 154 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099104 restraints weight = 46070.239| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.76 r_work: 0.3043 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26519 Z= 0.153 Angle : 0.687 16.205 36064 Z= 0.334 Chirality : 0.046 0.187 3986 Planarity : 0.005 0.097 4690 Dihedral : 5.960 62.132 3632 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.51 % Favored : 89.73 % Rotamer: Outliers : 4.65 % Allowed : 25.91 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.07 (0.15), residues: 3282 helix: 0.86 (0.28), residues: 374 sheet: -1.05 (0.16), residues: 1054 loop : -2.11 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP e 6 HIS 0.003 0.001 HIS J 282 PHE 0.015 0.001 PHE F 264 TYR 0.017 0.001 TYR Z 328 ARG 0.010 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 626) hydrogen bonds : angle 5.01542 ( 1608) metal coordination : bond 0.01077 ( 12) metal coordination : angle 7.36622 ( 36) SS BOND : bond 0.00760 ( 3) SS BOND : angle 2.99114 ( 6) covalent geometry : bond 0.00357 (26504) covalent geometry : angle 0.64531 (36022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 331 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8818 (tm-30) REVERT: E 99 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7541 (mm-30) REVERT: F 36 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: F 182 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8077 (ptm160) REVERT: F 264 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: F 287 MET cc_start: 0.9081 (tpp) cc_final: 0.8688 (tpp) REVERT: F 516 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7972 (p) REVERT: I 172 GLN cc_start: 0.5547 (OUTLIER) cc_final: 0.4598 (tm-30) REVERT: I 221 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6740 (mt) REVERT: J 16 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7144 (t0) REVERT: J 27 ILE cc_start: 0.9168 (mt) cc_final: 0.8862 (tt) REVERT: J 134 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7672 (tm-30) REVERT: J 183 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6420 (ttt180) REVERT: J 503 ARG cc_start: 0.8076 (ptt-90) cc_final: 0.7720 (ptt-90) REVERT: J 523 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8201 (mt) REVERT: J 600 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6949 (p0) REVERT: K 5 ARG cc_start: 0.7606 (mpp80) cc_final: 0.7396 (mpp80) REVERT: K 9 LYS cc_start: 0.7608 (mmtp) cc_final: 0.7158 (mmtp) REVERT: K 31 GLN cc_start: 0.8710 (mt0) cc_final: 0.8081 (mt0) REVERT: K 54 GLU cc_start: 0.8639 (tt0) cc_final: 0.8023 (tm-30) REVERT: K 64 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8093 (mp0) REVERT: K 97 ARG cc_start: 0.7553 (mmp-170) cc_final: 0.7275 (mmp-170) REVERT: L 1 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7475 (tmm) REVERT: L 59 TYR cc_start: 0.8623 (t80) cc_final: 0.8307 (t80) REVERT: L 214 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8148 (t80) REVERT: M 13 ASP cc_start: 0.8372 (m-30) cc_final: 0.7994 (t70) REVERT: M 27 ASP cc_start: 0.8028 (p0) cc_final: 0.7694 (p0) REVERT: M 64 GLU cc_start: 0.8852 (tp30) cc_final: 0.8278 (tm-30) REVERT: N 3 ASP cc_start: 0.7744 (p0) cc_final: 0.7426 (p0) REVERT: P 172 GLN cc_start: 0.7391 (mp10) cc_final: 0.6574 (tp40) REVERT: P 180 ASP cc_start: 0.8857 (t0) cc_final: 0.8476 (t0) REVERT: Y 27 ASP cc_start: 0.8381 (t0) cc_final: 0.8145 (t0) REVERT: Y 69 LYS cc_start: 0.8059 (tmtt) cc_final: 0.7626 (tmtt) REVERT: Z 36 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: Z 62 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7976 (p) REVERT: Z 179 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8745 (pt) REVERT: Z 272 MET cc_start: 0.8919 (tpp) cc_final: 0.8707 (tpt) REVERT: e 12 MET cc_start: 0.7945 (ttt) cc_final: 0.7662 (ttt) REVERT: e 59 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: e 95 MET cc_start: 0.6678 (tpp) cc_final: 0.6314 (tpp) REVERT: f 1 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8563 (tmm) REVERT: f 159 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: h 171 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7401 (mptt) REVERT: h 197 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8169 (ptp-170) REVERT: m 5 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6872 (mtm110) outliers start: 133 outliers final: 105 residues processed: 432 average time/residue: 0.4835 time to fit residues: 324.1594 Evaluate side-chains 452 residues out of total 2860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 327 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 518 THR Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 462 VAL Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 306 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 146 optimal weight: 0.0170 chunk 208 optimal weight: 0.7980 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099325 restraints weight = 46153.390| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.74 r_work: 0.3049 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 26519 Z= 0.173 Angle : 0.810 59.157 36064 Z= 0.435 Chirality : 0.045 0.165 3986 Planarity : 0.005 0.102 4690 Dihedral : 5.955 62.019 3632 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.75 % Favored : 89.55 % Rotamer: Outliers : 4.51 % Allowed : 26.08 % Favored : 69.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % 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: -2.07 (0.15), residues: 3282 helix: 0.87 (0.28), residues: 374 sheet: -1.05 (0.16), residues: 1054 loop : -2.11 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP e 6 HIS 0.003 0.001 HIS J 282 PHE 0.015 0.001 PHE F 264 TYR 0.015 0.001 TYR Z 328 ARG 0.017 0.000 ARG m 80 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 626) hydrogen bonds : angle 5.01537 ( 1608) metal coordination : bond 0.01079 ( 12) metal coordination : angle 7.36334 ( 36) SS BOND : bond 0.00642 ( 3) SS BOND : angle 2.83426 ( 6) covalent geometry : bond 0.00372 (26504) covalent geometry : angle 0.77593 (36022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16361.47 seconds wall clock time: 284 minutes 57.92 seconds (17097.92 seconds total)