Starting phenix.real_space_refine on Thu Jul 31 20:50:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywt_39644/07_2025/8ywt_39644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywt_39644/07_2025/8ywt_39644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywt_39644/07_2025/8ywt_39644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywt_39644/07_2025/8ywt_39644.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywt_39644/07_2025/8ywt_39644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywt_39644/07_2025/8ywt_39644.cif" } resolution = 2.8 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= 0.003 sd= 0.127 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 9026 2.51 5 N 2432 2.21 5 O 2504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13986 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 5089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5089 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 613} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 524 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "R" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "S" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "T" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "U" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "V" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 504 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "W" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "X" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Y" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Z" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "M" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 308} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 88 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 80 Classifications: {'peptide': 20} Incomplete info: {'backbone_only': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 8.34, per 1000 atoms: 0.60 Number of scatterers: 13986 At special positions: 0 Unit cell: (99.44, 124.96, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 2504 8.00 N 2432 7.00 C 9026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 6 sheets defined 81.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'N' and resid 20 through 31 Processing helix chain 'N' and resid 46 through 70 Processing helix chain 'N' and resid 83 through 129 Proline residue: N 93 - end of helix removed outlier: 4.592A pdb=" N GLU N 120 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Proline residue: N 121 - end of helix Processing helix chain 'N' and resid 131 through 135 Processing helix chain 'N' and resid 149 through 161 removed outlier: 3.668A pdb=" N VAL N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 197 Processing helix chain 'N' and resid 206 through 211 Processing helix chain 'N' and resid 212 through 266 removed outlier: 4.174A pdb=" N ARG N 218 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG N 219 " --> pdb=" O GLU N 215 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU N 220 " --> pdb=" O ALA N 216 " (cutoff:3.500A) Proline residue: N 228 - end of helix removed outlier: 5.723A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'N' and resid 286 through 296 removed outlier: 3.637A pdb=" N VAL N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG N 296 " --> pdb=" O GLU N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 334 Processing helix chain 'N' and resid 347 through 349 No H-bonds generated for 'chain 'N' and resid 347 through 349' Processing helix chain 'N' and resid 350 through 364 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 386 removed outlier: 3.526A pdb=" N GLY N 381 " --> pdb=" O ARG N 377 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR N 382 " --> pdb=" O TRP N 378 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 395 Processing helix chain 'N' and resid 399 through 424 removed outlier: 3.783A pdb=" N LYS N 405 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 435 Processing helix chain 'N' and resid 455 through 488 removed outlier: 6.317A pdb=" N ASN N 461 " --> pdb=" O ALA N 457 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU N 462 " --> pdb=" O LYS N 458 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE N 470 " --> pdb=" O LEU N 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 516 removed outlier: 3.555A pdb=" N GLU N 497 " --> pdb=" O ALA N 493 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 543 removed outlier: 3.987A pdb=" N TYR N 529 " --> pdb=" O GLN N 525 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 560 removed outlier: 4.990A pdb=" N PHE N 552 " --> pdb=" O ILE N 548 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 589 removed outlier: 3.570A pdb=" N GLY N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU N 589 " --> pdb=" O LEU N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 626 removed outlier: 4.934A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 4.072A pdb=" N LEU N 623 " --> pdb=" O GLN N 619 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU N 624 " --> pdb=" O PRO N 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 48 removed outlier: 4.079A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU O 47 " --> pdb=" O GLY O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 63 through 78 removed outlier: 3.759A pdb=" N GLY O 78 " --> pdb=" O PHE O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 48 removed outlier: 3.537A pdb=" N LEU P 10 " --> pdb=" O ALA P 6 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG P 12 " --> pdb=" O GLY P 8 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 16 " --> pdb=" O ARG P 12 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 78 Processing helix chain 'Q' and resid 8 through 48 removed outlier: 3.516A pdb=" N VAL Q 17 " --> pdb=" O GLY Q 13 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA Q 26 " --> pdb=" O ALA Q 22 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 Processing helix chain 'Q' and resid 64 through 78 Processing helix chain 'R' and resid 10 through 48 removed outlier: 3.620A pdb=" N ALA R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 Processing helix chain 'R' and resid 65 through 78 removed outlier: 3.576A pdb=" N GLY R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 48 removed outlier: 3.890A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA S 26 " --> pdb=" O ALA S 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA S 33 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN S 34 " --> pdb=" O THR S 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA S 35 " --> pdb=" O GLY S 31 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 65 through 78 Processing helix chain 'T' and resid 9 through 48 removed outlier: 3.598A pdb=" N LEU T 14 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA T 46 " --> pdb=" O VAL T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 Processing helix chain 'T' and resid 62 through 64 No H-bonds generated for 'chain 'T' and resid 62 through 64' Processing helix chain 'T' and resid 65 through 78 removed outlier: 3.558A pdb=" N GLY T 69 " --> pdb=" O LEU T 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 48 removed outlier: 4.433A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU U 47 " --> pdb=" O GLY U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'U' and resid 65 through 78 removed outlier: 3.512A pdb=" N GLY U 69 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE U 72 " --> pdb=" O PHE U 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 48 removed outlier: 3.585A pdb=" N ALA V 26 " --> pdb=" O ALA V 22 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 63 through 78 removed outlier: 3.537A pdb=" N PHE V 68 " --> pdb=" O THR V 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 46 removed outlier: 3.588A pdb=" N ALA W 16 " --> pdb=" O ARG W 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 50 No H-bonds generated for 'chain 'W' and resid 48 through 50' Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 63 through 78 Processing helix chain 'X' and resid 9 through 48 removed outlier: 3.598A pdb=" N LEU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL X 17 " --> pdb=" O GLY X 13 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY X 43 " --> pdb=" O ALA X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.996A pdb=" N PHE X 58 " --> pdb=" O THR X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 80 removed outlier: 3.769A pdb=" N GLY X 78 " --> pdb=" O PHE X 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG X 79 " --> pdb=" O ILE X 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 48 removed outlier: 4.368A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 62 through 64 No H-bonds generated for 'chain 'Y' and resid 62 through 64' Processing helix chain 'Y' and resid 65 through 78 removed outlier: 3.601A pdb=" N ILE Y 72 " --> pdb=" O PHE Y 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 48 removed outlier: 3.569A pdb=" N ALA Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY Z 43 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 Processing helix chain 'Z' and resid 64 through 80 removed outlier: 3.568A pdb=" N ARG Z 79 " --> pdb=" O ILE Z 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 17 removed outlier: 3.647A pdb=" N ALA M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 28 removed outlier: 4.170A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 32 through 42 removed outlier: 3.537A pdb=" N GLU M 42 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 48 removed outlier: 3.648A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 69 removed outlier: 3.515A pdb=" N LYS M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.879A pdb=" N VAL M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 106 removed outlier: 3.859A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU M 87 " --> pdb=" O ALA M 83 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU M 88 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 112 removed outlier: 3.650A pdb=" N VAL M 112 " --> pdb=" O PHE M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 129 Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 145 through 158 removed outlier: 4.180A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA M 153 " --> pdb=" O ARG M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 181 Processing helix chain 'M' and resid 185 through 207 removed outlier: 3.632A pdb=" N ARG M 189 " --> pdb=" O GLN M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 218 Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 238 through 243 Processing helix chain 'M' and resid 257 through 275 removed outlier: 3.798A pdb=" N CYS M 267 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS M 275 " --> pdb=" O LYS M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 279 Processing helix chain 'M' and resid 282 through 310 removed outlier: 4.373A pdb=" N VAL M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG M 305 " --> pdb=" O ARG M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 317 removed outlier: 4.648A pdb=" N VAL M 316 " --> pdb=" O PRO M 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 Processing helix chain 'K' and resid 32 through 41 Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 10 through 17 Processing helix chain 'L' and resid 18 through 21 removed outlier: 3.590A pdb=" N GLN L 21 " --> pdb=" O ALA L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 18 through 21' Processing sheet with id=AA1, first strand: chain 'N' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'N' and resid 14 through 15 Processing sheet with id=AA3, first strand: chain 'N' and resid 138 through 145 Processing sheet with id=AA4, first strand: chain 'N' and resid 318 through 319 Processing sheet with id=AA5, first strand: chain 'N' and resid 389 through 391 Processing sheet with id=AA6, first strand: chain 'N' and resid 438 through 439 1114 hydrogen bonds defined for protein. 3279 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: 4.06 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2300 1.27 - 1.41: 3332 1.41 - 1.54: 8259 1.54 - 1.68: 196 1.68 - 1.82: 46 Bond restraints: 14133 Sorted by residual: bond pdb=" C PRO R 62 " pdb=" O PRO R 62 " ideal model delta sigma weight residual 1.235 1.139 0.096 1.30e-02 5.92e+03 5.43e+01 bond pdb=" C PRO S 62 " pdb=" O PRO S 62 " ideal model delta sigma weight residual 1.235 1.143 0.092 1.30e-02 5.92e+03 5.06e+01 bond pdb=" C ALA S 33 " pdb=" O ALA S 33 " ideal model delta sigma weight residual 1.237 1.159 0.078 1.19e-02 7.06e+03 4.29e+01 bond pdb=" C PRO Q 62 " pdb=" O PRO Q 62 " ideal model delta sigma weight residual 1.238 1.157 0.081 1.42e-02 4.96e+03 3.22e+01 bond pdb=" CA ALA S 35 " pdb=" CB ALA S 35 " ideal model delta sigma weight residual 1.529 1.444 0.085 1.58e-02 4.01e+03 2.92e+01 ... (remaining 14128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 15774 2.56 - 5.13: 3158 5.13 - 7.69: 158 7.69 - 10.26: 22 10.26 - 12.82: 8 Bond angle restraints: 19120 Sorted by residual: angle pdb=" O VAL S 32 " pdb=" C VAL S 32 " pdb=" N ALA S 33 " ideal model delta sigma weight residual 121.87 109.13 12.74 9.70e-01 1.06e+00 1.72e+02 angle pdb=" CA VAL S 32 " pdb=" C VAL S 32 " pdb=" N ALA S 33 " ideal model delta sigma weight residual 117.15 129.97 -12.82 1.14e+00 7.69e-01 1.27e+02 angle pdb=" N ALA S 35 " pdb=" CA ALA S 35 " pdb=" C ALA S 35 " ideal model delta sigma weight residual 111.14 100.59 10.55 1.08e+00 8.57e-01 9.54e+01 angle pdb=" N LEU R 65 " pdb=" CA LEU R 65 " pdb=" C LEU R 65 " ideal model delta sigma weight residual 113.41 102.49 10.92 1.22e+00 6.72e-01 8.01e+01 angle pdb=" N THR Q 64 " pdb=" CA THR Q 64 " pdb=" C THR Q 64 " ideal model delta sigma weight residual 114.31 103.21 11.10 1.29e+00 6.01e-01 7.40e+01 ... (remaining 19115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 7460 17.40 - 34.79: 578 34.79 - 52.18: 139 52.18 - 69.58: 33 69.58 - 86.97: 12 Dihedral angle restraints: 8222 sinusoidal: 3106 harmonic: 5116 Sorted by residual: dihedral pdb=" C THR R 64 " pdb=" N THR R 64 " pdb=" CA THR R 64 " pdb=" CB THR R 64 " ideal model delta harmonic sigma weight residual -122.00 -105.35 -16.65 0 2.50e+00 1.60e-01 4.43e+01 dihedral pdb=" C LEU N 138 " pdb=" N LEU N 138 " pdb=" CA LEU N 138 " pdb=" CB LEU N 138 " ideal model delta harmonic sigma weight residual -122.60 -136.30 13.70 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" CA LEU N 204 " pdb=" C LEU N 204 " pdb=" N PRO N 205 " pdb=" CA PRO N 205 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 8219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1543 0.086 - 0.173: 572 0.173 - 0.259: 124 0.259 - 0.346: 16 0.346 - 0.432: 3 Chirality restraints: 2258 Sorted by residual: chirality pdb=" CA LEU N 138 " pdb=" N LEU N 138 " pdb=" C LEU N 138 " pdb=" CB LEU N 138 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA ARG M 266 " pdb=" N ARG M 266 " pdb=" C ARG M 266 " pdb=" CB ARG M 266 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASP N 163 " pdb=" N ASP N 163 " pdb=" C ASP N 163 " pdb=" CB ASP N 163 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2255 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 118 " 0.150 2.00e-02 2.50e+03 8.54e-02 1.46e+02 pdb=" CG TYR N 118 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR N 118 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR N 118 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR N 118 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR N 118 " -0.059 2.00e-02 2.50e+03 pdb=" CZ TYR N 118 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR N 118 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 616 " -0.114 2.00e-02 2.50e+03 8.53e-02 1.09e+02 pdb=" CG HIS N 616 " 0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS N 616 " 0.066 2.00e-02 2.50e+03 pdb=" CD2 HIS N 616 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 HIS N 616 " -0.073 2.00e-02 2.50e+03 pdb=" NE2 HIS N 616 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 43 " -0.112 2.00e-02 2.50e+03 5.94e-02 7.05e+01 pdb=" CG TYR N 43 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR N 43 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR N 43 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR N 43 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR N 43 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR N 43 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR N 43 " -0.087 2.00e-02 2.50e+03 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 649 2.76 - 3.30: 14428 3.30 - 3.83: 21447 3.83 - 4.37: 29777 4.37 - 4.90: 48292 Nonbonded interactions: 114593 Sorted by model distance: nonbonded pdb=" O HOH N 702 " pdb=" O HOH N 719 " model vdw 2.228 3.040 nonbonded pdb=" NH1 ARG N 622 " pdb=" OE2 GLU N 627 " model vdw 2.233 3.120 nonbonded pdb=" O HOH M 403 " pdb=" O HOH M 416 " model vdw 2.281 3.040 nonbonded pdb=" O ILE N 317 " pdb=" O HOH N 701 " model vdw 2.314 3.040 nonbonded pdb=" OE2 GLU N 426 " pdb=" O HOH N 702 " model vdw 2.331 3.040 ... (remaining 114588 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 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = chain 'V' selection = (chain 'W' and resid 9 through 80) selection = (chain 'X' and resid 9 through 80) selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.100 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 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 : 0.013 0.103 14134 Z= 0.815 Angle : 1.926 12.824 19122 Z= 1.327 Chirality : 0.091 0.432 2258 Planarity : 0.019 0.303 2459 Dihedral : 14.343 86.972 5007 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.09 % Favored : 97.64 % Rotamer: Outliers : 3.36 % Allowed : 6.64 % Favored : 90.01 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 1863 helix: -0.89 (0.12), residues: 1411 sheet: -1.18 (0.71), residues: 55 loop : -0.38 (0.34), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.019 TRP N 545 HIS 0.013 0.004 HIS N 297 PHE 0.070 0.013 PHE X 68 TYR 0.150 0.024 TYR N 118 ARG 0.013 0.001 ARG M 266 Details of bonding type rmsd hydrogen bonds : bond 0.22015 ( 1114) hydrogen bonds : angle 7.07015 ( 3279) SS BOND : bond 0.02114 ( 1) SS BOND : angle 2.57436 ( 2) covalent geometry : bond 0.01260 (14133) covalent geometry : angle 1.92554 (19120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.511 Fit side-chains REVERT: N 155 GLU cc_start: 0.6652 (tt0) cc_final: 0.5848 (tm-30) REVERT: N 306 GLU cc_start: 0.6246 (mt-10) cc_final: 0.6041 (mm-30) REVERT: N 322 ASP cc_start: 0.6111 (t0) cc_final: 0.5886 (t0) REVERT: N 401 GLN cc_start: 0.6985 (tt0) cc_final: 0.6279 (mp10) REVERT: N 544 ILE cc_start: 0.6305 (mt) cc_final: 0.6057 (mt) REVERT: N 606 LEU cc_start: 0.6563 (tt) cc_final: 0.6362 (tp) REVERT: N 622 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7455 (ptm160) REVERT: U 30 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7945 (m) REVERT: Y 11 ASP cc_start: 0.6852 (t0) cc_final: 0.6310 (t70) REVERT: M 21 LYS cc_start: 0.6540 (mtpt) cc_final: 0.6288 (pttm) REVERT: M 232 ARG cc_start: 0.6809 (mtm110) cc_final: 0.6219 (ttp-170) REVERT: M 291 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5598 (mmtt) outliers start: 45 outliers final: 8 residues processed: 252 average time/residue: 1.1552 time to fit residues: 321.4158 Evaluate side-chains 127 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 567 VAL Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain R residue 62 PRO Chi-restraints excluded: chain S residue 62 PRO Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 291 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 25 GLN N 106 GLN N 250 GLN N 408 HIS N 525 GLN R 51 ASN T 51 ASN U 51 ASN W 51 ASN X 34 GLN X 51 ASN M 91 ASN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116676 restraints weight = 14620.905| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.76 r_work: 0.3360 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14134 Z= 0.175 Angle : 0.691 9.134 19122 Z= 0.351 Chirality : 0.043 0.217 2258 Planarity : 0.006 0.063 2459 Dihedral : 5.384 56.212 2050 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.03 % Allowed : 11.26 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1863 helix: 1.01 (0.13), residues: 1433 sheet: -1.73 (0.72), residues: 47 loop : 0.74 (0.38), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 625 HIS 0.006 0.001 HIS N 491 PHE 0.015 0.002 PHE N 470 TYR 0.012 0.002 TYR N 118 ARG 0.010 0.001 ARG M 90 Details of bonding type rmsd hydrogen bonds : bond 0.05902 ( 1114) hydrogen bonds : angle 3.99500 ( 3279) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.60480 ( 2) covalent geometry : bond 0.00374 (14133) covalent geometry : angle 0.69063 (19120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 180 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: N 50 ARG cc_start: 0.6272 (mtt90) cc_final: 0.5664 (mmp80) REVERT: N 120 GLU cc_start: 0.6406 (tt0) cc_final: 0.6113 (mp0) REVERT: N 155 GLU cc_start: 0.6675 (tt0) cc_final: 0.5840 (tm-30) REVERT: N 233 GLU cc_start: 0.7069 (tp30) cc_final: 0.6181 (tt0) REVERT: N 306 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6453 (mm-30) REVERT: N 401 GLN cc_start: 0.7047 (tt0) cc_final: 0.6441 (mp10) REVERT: N 413 MET cc_start: 0.8199 (mtp) cc_final: 0.7917 (mtp) REVERT: N 453 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7026 (ttp-170) REVERT: N 484 TYR cc_start: 0.7466 (t80) cc_final: 0.7206 (t80) REVERT: N 598 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6646 (mt) REVERT: N 606 LEU cc_start: 0.6795 (tt) cc_final: 0.6568 (mp) REVERT: N 627 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: N 638 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7898 (m-40) REVERT: P 12 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6773 (mtm110) REVERT: Q 12 ARG cc_start: 0.6994 (mtp180) cc_final: 0.6377 (mtp85) REVERT: X 12 ARG cc_start: 0.6984 (tpt170) cc_final: 0.6518 (mtp85) REVERT: M 21 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7343 (mttt) REVERT: M 85 ARG cc_start: 0.6391 (ttp80) cc_final: 0.6088 (ttt-90) REVERT: M 111 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7344 (tt0) REVERT: M 120 ARG cc_start: 0.7177 (mtt-85) cc_final: 0.6773 (mtt-85) REVERT: M 149 ARG cc_start: 0.6608 (ttm170) cc_final: 0.5751 (ttp80) REVERT: M 181 LYS cc_start: 0.6634 (ptpt) cc_final: 0.6391 (ptpt) REVERT: M 205 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.5217 (t80) REVERT: M 220 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7530 (mptt) REVERT: M 291 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7348 (mmpt) outliers start: 54 outliers final: 9 residues processed: 224 average time/residue: 1.5599 time to fit residues: 377.3434 Evaluate side-chains 141 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 308 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 627 GLU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 291 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 44 optimal weight: 0.9990 chunk 146 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 25 GLN N 250 GLN N 311 HIS N 323 ASN M 94 HIS M 145 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108162 restraints weight = 14843.742| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.66 r_work: 0.3232 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14134 Z= 0.157 Angle : 0.595 8.131 19122 Z= 0.303 Chirality : 0.040 0.149 2258 Planarity : 0.005 0.068 2459 Dihedral : 4.840 66.734 2032 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.40 % Allowed : 14.24 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.20), residues: 1863 helix: 1.70 (0.13), residues: 1432 sheet: -1.65 (0.76), residues: 45 loop : 0.44 (0.36), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 295 HIS 0.006 0.001 HIS N 557 PHE 0.016 0.001 PHE M 172 TYR 0.016 0.001 TYR M 7 ARG 0.008 0.001 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.06313 ( 1114) hydrogen bonds : angle 3.82406 ( 3279) SS BOND : bond 0.00337 ( 1) SS BOND : angle 1.84008 ( 2) covalent geometry : bond 0.00340 (14133) covalent geometry : angle 0.59512 (19120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 1.384 Fit side-chains REVERT: N 6 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: N 50 ARG cc_start: 0.6405 (mtt90) cc_final: 0.5760 (mtp180) REVERT: N 116 GLN cc_start: 0.7019 (pt0) cc_final: 0.6533 (mt0) REVERT: N 120 GLU cc_start: 0.6498 (tt0) cc_final: 0.6136 (mp0) REVERT: N 147 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7169 (mm-30) REVERT: N 155 GLU cc_start: 0.6920 (tt0) cc_final: 0.6041 (tm-30) REVERT: N 229 ARG cc_start: 0.6596 (mtm110) cc_final: 0.6336 (mtm-85) REVERT: N 233 GLU cc_start: 0.7186 (tp30) cc_final: 0.6275 (mt-10) REVERT: N 236 GLN cc_start: 0.6711 (mp10) cc_final: 0.6502 (mm110) REVERT: N 306 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6593 (mm-30) REVERT: N 311 HIS cc_start: 0.5148 (m90) cc_final: 0.4273 (t70) REVERT: N 401 GLN cc_start: 0.7439 (tt0) cc_final: 0.6495 (mp10) REVERT: N 413 MET cc_start: 0.8282 (mtp) cc_final: 0.8050 (mtp) REVERT: N 446 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7541 (mt) REVERT: N 453 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7796 (ttp-170) REVERT: N 484 TYR cc_start: 0.7853 (t80) cc_final: 0.7613 (t80) REVERT: N 492 MET cc_start: 0.8020 (mmm) cc_final: 0.7665 (mmt) REVERT: N 515 TYR cc_start: 0.5396 (m-80) cc_final: 0.5163 (m-80) REVERT: N 525 GLN cc_start: 0.7151 (tp40) cc_final: 0.6764 (tp40) REVERT: N 543 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6539 (mtp85) REVERT: N 598 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6833 (mt) REVERT: N 606 LEU cc_start: 0.6835 (tt) cc_final: 0.6481 (mt) REVERT: O 47 GLU cc_start: 0.6923 (tp30) cc_final: 0.6222 (tt0) REVERT: P 12 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6712 (mtm110) REVERT: Q 12 ARG cc_start: 0.6727 (mtp180) cc_final: 0.6238 (mtp85) REVERT: S 47 GLU cc_start: 0.6210 (mt-10) cc_final: 0.5808 (tt0) REVERT: S 63 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8331 (mm-30) REVERT: V 49 ARG cc_start: 0.7716 (mpt180) cc_final: 0.7299 (mmm160) REVERT: X 12 ARG cc_start: 0.6916 (tpt170) cc_final: 0.6536 (mtp85) REVERT: X 75 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7295 (mm) REVERT: Z 12 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.5751 (ttp80) REVERT: Z 47 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: M 21 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7583 (mttt) REVERT: M 59 ARG cc_start: 0.7214 (ttp-170) cc_final: 0.6781 (ttp80) REVERT: M 67 LYS cc_start: 0.8054 (mtpm) cc_final: 0.7214 (ptpt) REVERT: M 71 ASP cc_start: 0.8054 (p0) cc_final: 0.7505 (p0) REVERT: M 85 ARG cc_start: 0.6565 (ttp80) cc_final: 0.6265 (ttt-90) REVERT: M 111 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7462 (tt0) REVERT: M 190 ASP cc_start: 0.6829 (t0) cc_final: 0.6372 (m-30) REVERT: M 220 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7583 (mttt) REVERT: M 227 ARG cc_start: 0.6707 (mtt-85) cc_final: 0.6412 (mtt-85) REVERT: M 301 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6699 (ttt90) outliers start: 59 outliers final: 14 residues processed: 204 average time/residue: 1.5537 time to fit residues: 341.8615 Evaluate side-chains 156 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 159 GLN Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 130 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 44 GLN N 65 HIS N 605 HIS V 51 ASN M 26 GLN M 94 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099951 restraints weight = 14869.911| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.69 r_work: 0.3130 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14134 Z= 0.231 Angle : 0.696 9.193 19122 Z= 0.346 Chirality : 0.044 0.176 2258 Planarity : 0.006 0.068 2459 Dihedral : 5.005 77.653 2028 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.00 % Allowed : 13.65 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 1863 helix: 1.43 (0.13), residues: 1431 sheet: -1.79 (0.69), residues: 48 loop : 0.07 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 295 HIS 0.008 0.001 HIS N 557 PHE 0.019 0.002 PHE M 172 TYR 0.020 0.002 TYR N 43 ARG 0.007 0.001 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.07447 ( 1114) hydrogen bonds : angle 3.98814 ( 3279) SS BOND : bond 0.00454 ( 1) SS BOND : angle 2.09356 ( 2) covalent geometry : bond 0.00575 (14133) covalent geometry : angle 0.69570 (19120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6921 (mpt90) cc_final: 0.6176 (mtm110) REVERT: N 120 GLU cc_start: 0.6692 (tt0) cc_final: 0.6252 (mp0) REVERT: N 147 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7355 (mm-30) REVERT: N 155 GLU cc_start: 0.6657 (tt0) cc_final: 0.5952 (tm-30) REVERT: N 159 LYS cc_start: 0.6900 (mtmt) cc_final: 0.6497 (tptt) REVERT: N 215 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: N 218 ARG cc_start: 0.7363 (ttp80) cc_final: 0.6979 (mtm110) REVERT: N 229 ARG cc_start: 0.6653 (mtm110) cc_final: 0.6360 (mtm-85) REVERT: N 233 GLU cc_start: 0.7074 (tp30) cc_final: 0.6300 (mt-10) REVERT: N 306 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6654 (mm-30) REVERT: N 311 HIS cc_start: 0.5837 (m90) cc_final: 0.4757 (t70) REVERT: N 344 THR cc_start: 0.7695 (m) cc_final: 0.7440 (p) REVERT: N 397 LYS cc_start: 0.7485 (tttt) cc_final: 0.7238 (tmtt) REVERT: N 401 GLN cc_start: 0.7673 (tt0) cc_final: 0.6667 (mp10) REVERT: N 413 MET cc_start: 0.8460 (mtp) cc_final: 0.8231 (mtp) REVERT: N 453 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7866 (ttp-170) REVERT: N 484 TYR cc_start: 0.7789 (t80) cc_final: 0.7535 (t80) REVERT: N 490 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6619 (mpp-170) REVERT: N 492 MET cc_start: 0.8039 (mmm) cc_final: 0.7790 (mmt) REVERT: N 598 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6998 (mt) REVERT: N 606 LEU cc_start: 0.7029 (tt) cc_final: 0.6637 (mt) REVERT: O 49 ARG cc_start: 0.7656 (mpt180) cc_final: 0.7444 (mtp180) REVERT: P 12 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6557 (mtm110) REVERT: Q 12 ARG cc_start: 0.6917 (mtp180) cc_final: 0.6322 (mtp85) REVERT: S 63 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8447 (mm-30) REVERT: U 49 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.7001 (mmm160) REVERT: V 49 ARG cc_start: 0.7901 (mpt180) cc_final: 0.7523 (mmm160) REVERT: X 12 ARG cc_start: 0.6965 (tpt170) cc_final: 0.6684 (mtp85) REVERT: Y 47 GLU cc_start: 0.7931 (tp30) cc_final: 0.7539 (tp30) REVERT: Z 47 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: M 30 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6921 (m-30) REVERT: M 59 ARG cc_start: 0.7321 (ttp-170) cc_final: 0.6665 (ttp80) REVERT: M 71 ASP cc_start: 0.8128 (p0) cc_final: 0.7621 (p0) REVERT: M 111 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7518 (tt0) REVERT: M 171 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6496 (mtp180) REVERT: M 190 ASP cc_start: 0.6736 (t0) cc_final: 0.6491 (m-30) REVERT: M 220 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7546 (mttt) REVERT: M 301 ARG cc_start: 0.7405 (mmm160) cc_final: 0.6696 (ttt90) outliers start: 67 outliers final: 26 residues processed: 202 average time/residue: 1.9068 time to fit residues: 416.0697 Evaluate side-chains 179 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 LYS Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 237 HIS Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 159 GLN Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 605 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105163 restraints weight = 14914.421| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.70 r_work: 0.3208 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14134 Z= 0.133 Angle : 0.523 8.302 19122 Z= 0.267 Chirality : 0.038 0.148 2258 Planarity : 0.005 0.063 2459 Dihedral : 4.657 78.328 2028 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.58 % Allowed : 15.73 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 1863 helix: 1.91 (0.13), residues: 1442 sheet: -1.90 (0.67), residues: 48 loop : 0.10 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.006 0.001 HIS M 94 PHE 0.019 0.001 PHE N 427 TYR 0.015 0.001 TYR N 43 ARG 0.009 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.05269 ( 1114) hydrogen bonds : angle 3.57842 ( 3279) SS BOND : bond 0.00514 ( 1) SS BOND : angle 2.74210 ( 2) covalent geometry : bond 0.00290 (14133) covalent geometry : angle 0.52224 (19120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: N 50 ARG cc_start: 0.6438 (mtt90) cc_final: 0.5842 (mtp85) REVERT: N 54 ARG cc_start: 0.6777 (mpt90) cc_final: 0.6121 (mtm110) REVERT: N 66 THR cc_start: 0.8468 (t) cc_final: 0.8175 (m) REVERT: N 75 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: N 120 GLU cc_start: 0.6495 (tt0) cc_final: 0.6066 (mp0) REVERT: N 147 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7256 (mm-30) REVERT: N 155 GLU cc_start: 0.6605 (tt0) cc_final: 0.5918 (tm-30) REVERT: N 215 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: N 218 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7212 (mtm110) REVERT: N 229 ARG cc_start: 0.6585 (mtm110) cc_final: 0.6325 (mtt180) REVERT: N 237 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6913 (m-70) REVERT: N 306 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6566 (mm-30) REVERT: N 309 ASP cc_start: 0.6331 (t0) cc_final: 0.6115 (p0) REVERT: N 311 HIS cc_start: 0.5580 (m90) cc_final: 0.4661 (t70) REVERT: N 397 LYS cc_start: 0.7528 (tttt) cc_final: 0.7232 (tmtt) REVERT: N 401 GLN cc_start: 0.7321 (tt0) cc_final: 0.6342 (mp10) REVERT: N 413 MET cc_start: 0.8235 (mtp) cc_final: 0.8018 (mtp) REVERT: N 446 LEU cc_start: 0.8191 (tp) cc_final: 0.7700 (mp) REVERT: N 453 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7696 (ttp-170) REVERT: N 484 TYR cc_start: 0.7710 (t80) cc_final: 0.7472 (t80) REVERT: N 492 MET cc_start: 0.8050 (mmm) cc_final: 0.7814 (mmt) REVERT: N 543 ARG cc_start: 0.7065 (mtp85) cc_final: 0.6766 (mtp85) REVERT: N 598 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6773 (mt) REVERT: N 606 LEU cc_start: 0.6986 (tt) cc_final: 0.6626 (mt) REVERT: O 47 GLU cc_start: 0.7200 (tp30) cc_final: 0.6449 (tt0) REVERT: O 79 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7269 (mmt90) REVERT: P 12 ARG cc_start: 0.7057 (mtt180) cc_final: 0.6520 (mtm110) REVERT: S 47 GLU cc_start: 0.6287 (mt-10) cc_final: 0.5814 (tt0) REVERT: S 63 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8418 (mm-30) REVERT: V 49 ARG cc_start: 0.7869 (mpt180) cc_final: 0.7451 (mmm160) REVERT: W 79 ARG cc_start: 0.6939 (mtt-85) cc_final: 0.6549 (mtp85) REVERT: X 12 ARG cc_start: 0.7032 (tpt170) cc_final: 0.6673 (mtp85) REVERT: Y 47 GLU cc_start: 0.7896 (tp30) cc_final: 0.7577 (tp30) REVERT: Z 47 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: M 59 ARG cc_start: 0.7242 (ttp-170) cc_final: 0.6635 (ttp-110) REVERT: M 67 LYS cc_start: 0.7950 (mtpm) cc_final: 0.7286 (ptpt) REVERT: M 71 ASP cc_start: 0.8047 (p0) cc_final: 0.7565 (p0) REVERT: M 111 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7551 (tt0) REVERT: M 171 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6459 (mtp180) REVERT: M 220 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7573 (mttt) REVERT: M 301 ARG cc_start: 0.7321 (mmm160) cc_final: 0.6997 (ttm-80) outliers start: 48 outliers final: 15 residues processed: 184 average time/residue: 1.9682 time to fit residues: 391.9251 Evaluate side-chains 162 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 237 HIS Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 297 HIS O 51 ASN M 26 GLN M 94 HIS ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100507 restraints weight = 14958.449| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.68 r_work: 0.3143 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14134 Z= 0.190 Angle : 0.604 7.896 19122 Z= 0.303 Chirality : 0.041 0.164 2258 Planarity : 0.005 0.063 2459 Dihedral : 4.776 79.824 2028 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.18 % Allowed : 15.06 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1863 helix: 1.79 (0.13), residues: 1440 sheet: -1.77 (0.66), residues: 48 loop : -0.09 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.006 0.001 HIS N 557 PHE 0.015 0.001 PHE M 172 TYR 0.020 0.001 TYR N 43 ARG 0.008 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.06594 ( 1114) hydrogen bonds : angle 3.76607 ( 3279) SS BOND : bond 0.00170 ( 1) SS BOND : angle 3.13041 ( 2) covalent geometry : bond 0.00466 (14133) covalent geometry : angle 0.60284 (19120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6852 (mpt90) cc_final: 0.6141 (mtm110) REVERT: N 66 THR cc_start: 0.8491 (t) cc_final: 0.8104 (m) REVERT: N 75 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: N 120 GLU cc_start: 0.6561 (tt0) cc_final: 0.6113 (mp0) REVERT: N 147 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7291 (mm-30) REVERT: N 155 GLU cc_start: 0.6712 (tt0) cc_final: 0.5938 (tm-30) REVERT: N 215 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: N 218 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7235 (mtm110) REVERT: N 229 ARG cc_start: 0.6568 (mtm110) cc_final: 0.6132 (mtt180) REVERT: N 233 GLU cc_start: 0.7086 (tp30) cc_final: 0.6345 (mt-10) REVERT: N 237 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6901 (m-70) REVERT: N 306 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6536 (mm-30) REVERT: N 309 ASP cc_start: 0.6498 (t0) cc_final: 0.6201 (p0) REVERT: N 311 HIS cc_start: 0.5841 (m90) cc_final: 0.4847 (t70) REVERT: N 397 LYS cc_start: 0.7571 (tttt) cc_final: 0.7256 (tmtt) REVERT: N 401 GLN cc_start: 0.7584 (tt0) cc_final: 0.6548 (mp10) REVERT: N 413 MET cc_start: 0.8448 (mtp) cc_final: 0.8145 (mtp) REVERT: N 453 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7732 (ttp-170) REVERT: N 484 TYR cc_start: 0.7796 (t80) cc_final: 0.7562 (t80) REVERT: N 543 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6788 (mtp85) REVERT: N 606 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6645 (mt) REVERT: O 79 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7381 (mmt90) REVERT: P 12 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6596 (mtm110) REVERT: Q 12 ARG cc_start: 0.6931 (mtp180) cc_final: 0.6308 (mtp85) REVERT: Q 49 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7559 (ttm-80) REVERT: S 47 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5877 (tt0) REVERT: S 63 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8445 (mm-30) REVERT: V 49 ARG cc_start: 0.7893 (mpt180) cc_final: 0.7458 (mmm160) REVERT: W 79 ARG cc_start: 0.6990 (mtt-85) cc_final: 0.6582 (mtp85) REVERT: X 12 ARG cc_start: 0.6935 (tpt170) cc_final: 0.6612 (mtp85) REVERT: Z 47 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: M 30 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: M 52 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: M 59 ARG cc_start: 0.7301 (ttp-170) cc_final: 0.6648 (ttp80) REVERT: M 71 ASP cc_start: 0.8191 (p0) cc_final: 0.7704 (p0) REVERT: M 85 ARG cc_start: 0.6917 (ttp80) cc_final: 0.6587 (ttt-90) REVERT: M 111 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7551 (tt0) REVERT: M 171 ARG cc_start: 0.7259 (mtt90) cc_final: 0.6499 (mtp180) REVERT: M 190 ASP cc_start: 0.6756 (t0) cc_final: 0.6487 (m-30) REVERT: M 220 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7646 (mttt) REVERT: M 301 ARG cc_start: 0.7467 (mmm160) cc_final: 0.7044 (ttm-80) outliers start: 56 outliers final: 28 residues processed: 185 average time/residue: 1.9310 time to fit residues: 386.7528 Evaluate side-chains 181 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 LYS Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 237 HIS Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 226 ASP Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 182 optimal weight: 50.0000 chunk 32 optimal weight: 0.3980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 26 GLN ** M 126 GLN ** 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 = 0.3788 r_free = 0.3788 target = 0.151188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111095 restraints weight = 15325.102| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.59 r_work: 0.3283 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.7634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14134 Z= 0.159 Angle : 0.556 8.326 19122 Z= 0.281 Chirality : 0.039 0.157 2258 Planarity : 0.005 0.060 2459 Dihedral : 4.699 80.476 2028 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.21 % Allowed : 16.33 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 1863 helix: 1.94 (0.13), residues: 1435 sheet: -1.55 (0.67), residues: 48 loop : -0.19 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.004 0.001 HIS N 557 PHE 0.013 0.001 PHE N 427 TYR 0.020 0.001 TYR N 43 ARG 0.010 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.05909 ( 1114) hydrogen bonds : angle 3.65478 ( 3279) SS BOND : bond 0.00384 ( 1) SS BOND : angle 5.47195 ( 2) covalent geometry : bond 0.00373 (14133) covalent geometry : angle 0.55351 (19120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 1.739 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.7174 (mpt90) cc_final: 0.6589 (mtm110) REVERT: N 66 THR cc_start: 0.8689 (t) cc_final: 0.8346 (m) REVERT: N 75 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: N 120 GLU cc_start: 0.6756 (tt0) cc_final: 0.6499 (mp0) REVERT: N 147 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7361 (mm-30) REVERT: N 155 GLU cc_start: 0.7037 (tt0) cc_final: 0.6225 (tm-30) REVERT: N 215 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: N 218 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7541 (mtm110) REVERT: N 229 ARG cc_start: 0.6773 (mtm110) cc_final: 0.6420 (mtt180) REVERT: N 233 GLU cc_start: 0.7350 (tp30) cc_final: 0.6683 (mt-10) REVERT: N 306 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6764 (mm-30) REVERT: N 309 ASP cc_start: 0.6580 (t0) cc_final: 0.6348 (p0) REVERT: N 311 HIS cc_start: 0.5937 (m90) cc_final: 0.5016 (t70) REVERT: N 384 LYS cc_start: 0.7458 (tmmt) cc_final: 0.7241 (tttp) REVERT: N 397 LYS cc_start: 0.7767 (tttt) cc_final: 0.7536 (tmtt) REVERT: N 401 GLN cc_start: 0.7606 (tt0) cc_final: 0.6762 (mp10) REVERT: N 413 MET cc_start: 0.8598 (mtp) cc_final: 0.8340 (mtp) REVERT: N 453 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7911 (ttp-170) REVERT: N 543 ARG cc_start: 0.7297 (mtp85) cc_final: 0.7068 (mtp85) REVERT: N 606 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7082 (mt) REVERT: N 608 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6449 (mp) REVERT: O 47 GLU cc_start: 0.7520 (tp30) cc_final: 0.6906 (tt0) REVERT: O 79 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7593 (mmt90) REVERT: P 12 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7073 (mtm110) REVERT: P 49 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7211 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7640 (mtp85) REVERT: U 49 ARG cc_start: 0.7928 (mpt90) cc_final: 0.7243 (mmm160) REVERT: V 49 ARG cc_start: 0.7984 (mpt180) cc_final: 0.7643 (mmm160) REVERT: W 63 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8028 (mm-30) REVERT: W 79 ARG cc_start: 0.7317 (mtt-85) cc_final: 0.6929 (mtp85) REVERT: X 64 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8023 (p) REVERT: Y 47 GLU cc_start: 0.8146 (tp30) cc_final: 0.7786 (tp30) REVERT: Z 47 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: M 30 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: M 59 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7145 (ttp-110) REVERT: M 65 GLN cc_start: 0.8612 (mt0) cc_final: 0.8355 (mm-40) REVERT: M 67 LYS cc_start: 0.8251 (mtpm) cc_final: 0.7559 (ptpt) REVERT: M 71 ASP cc_start: 0.8194 (p0) cc_final: 0.7716 (p0) REVERT: M 85 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6928 (ttt-90) REVERT: M 111 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7775 (tt0) REVERT: M 171 ARG cc_start: 0.7620 (mtt90) cc_final: 0.6978 (mtp180) REVERT: M 189 ARG cc_start: 0.6827 (ttm110) cc_final: 0.6354 (mmm-85) REVERT: M 220 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7918 (mttt) REVERT: M 301 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7434 (ttm-80) outliers start: 43 outliers final: 17 residues processed: 181 average time/residue: 1.9570 time to fit residues: 379.3148 Evaluate side-chains 175 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 608 ILE Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 111 optimal weight: 0.0060 chunk 103 optimal weight: 6.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 183 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107739 restraints weight = 14250.244| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.67 r_work: 0.3140 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14134 Z= 0.122 Angle : 0.497 8.274 19122 Z= 0.254 Chirality : 0.037 0.155 2258 Planarity : 0.005 0.055 2459 Dihedral : 4.514 80.157 2028 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.39 % Allowed : 17.67 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.20), residues: 1863 helix: 2.23 (0.14), residues: 1438 sheet: -1.30 (0.69), residues: 48 loop : -0.17 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 PHE 0.012 0.001 PHE N 427 TYR 0.015 0.001 TYR N 43 ARG 0.007 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 1114) hydrogen bonds : angle 3.49804 ( 3279) SS BOND : bond 0.00323 ( 1) SS BOND : angle 2.81740 ( 2) covalent geometry : bond 0.00261 (14133) covalent geometry : angle 0.49616 (19120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.7293 (mpt90) cc_final: 0.6643 (mtm110) REVERT: N 66 THR cc_start: 0.8760 (t) cc_final: 0.8462 (m) REVERT: N 120 GLU cc_start: 0.6760 (tt0) cc_final: 0.6327 (mp0) REVERT: N 147 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7468 (mm-30) REVERT: N 155 GLU cc_start: 0.6987 (tt0) cc_final: 0.6231 (tm-30) REVERT: N 218 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7480 (mtm110) REVERT: N 306 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6863 (mm-30) REVERT: N 309 ASP cc_start: 0.6601 (t0) cc_final: 0.6344 (p0) REVERT: N 311 HIS cc_start: 0.5863 (m90) cc_final: 0.4972 (t70) REVERT: N 384 LYS cc_start: 0.7531 (tmmt) cc_final: 0.7306 (tttp) REVERT: N 401 GLN cc_start: 0.7510 (tt0) cc_final: 0.6687 (mp10) REVERT: N 413 MET cc_start: 0.8659 (mtp) cc_final: 0.8458 (mtp) REVERT: N 453 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7946 (ttp-170) REVERT: N 490 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6863 (mpp-170) REVERT: N 606 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7111 (mt) REVERT: O 47 GLU cc_start: 0.7635 (tp30) cc_final: 0.7059 (tt0) REVERT: O 79 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7801 (mmt90) REVERT: P 12 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7178 (mtm110) REVERT: P 49 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7178 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7698 (mtp85) REVERT: T 49 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7735 (mmm160) REVERT: U 49 ARG cc_start: 0.8069 (mpt90) cc_final: 0.7410 (mmm160) REVERT: V 49 ARG cc_start: 0.8079 (mpt180) cc_final: 0.7855 (tpp-160) REVERT: W 79 ARG cc_start: 0.7219 (mtt-85) cc_final: 0.6992 (mtp85) REVERT: Y 47 GLU cc_start: 0.8265 (tp30) cc_final: 0.7932 (tp30) REVERT: Z 47 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: M 30 ASP cc_start: 0.7672 (p0) cc_final: 0.7370 (m-30) REVERT: M 59 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7296 (ttp-110) REVERT: M 65 GLN cc_start: 0.8586 (mt0) cc_final: 0.8349 (mm-40) REVERT: M 67 LYS cc_start: 0.8221 (mtpm) cc_final: 0.7712 (ptpt) REVERT: M 71 ASP cc_start: 0.8283 (p0) cc_final: 0.7792 (p0) REVERT: M 85 ARG cc_start: 0.7262 (ttp80) cc_final: 0.6940 (ttt-90) REVERT: M 111 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7942 (tt0) REVERT: M 171 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7141 (mtp180) REVERT: M 220 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8029 (mttt) REVERT: M 301 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7589 (ttm-80) outliers start: 32 outliers final: 16 residues processed: 176 average time/residue: 1.7279 time to fit residues: 325.4765 Evaluate side-chains 163 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 189 GLN N 338 ASN M 26 GLN M 94 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106997 restraints weight = 14039.959| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.60 r_work: 0.3085 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14134 Z= 0.165 Angle : 0.562 8.358 19122 Z= 0.284 Chirality : 0.039 0.161 2258 Planarity : 0.005 0.059 2459 Dihedral : 4.616 80.705 2028 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.76 % Allowed : 17.45 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1863 helix: 2.03 (0.13), residues: 1437 sheet: -1.36 (0.69), residues: 48 loop : -0.29 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 295 HIS 0.005 0.001 HIS N 557 PHE 0.014 0.001 PHE M 218 TYR 0.019 0.001 TYR N 43 ARG 0.010 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.06026 ( 1114) hydrogen bonds : angle 3.67100 ( 3279) SS BOND : bond 0.00884 ( 1) SS BOND : angle 3.53475 ( 2) covalent geometry : bond 0.00393 (14133) covalent geometry : angle 0.56088 (19120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.7390 (mpt90) cc_final: 0.6703 (mtm110) REVERT: N 66 THR cc_start: 0.8790 (t) cc_final: 0.8431 (m) REVERT: N 120 GLU cc_start: 0.6912 (tt0) cc_final: 0.6507 (mp0) REVERT: N 147 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7484 (mm-30) REVERT: N 155 GLU cc_start: 0.7134 (tt0) cc_final: 0.6341 (tm-30) REVERT: N 218 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7564 (mtm110) REVERT: N 306 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6880 (mm-30) REVERT: N 309 ASP cc_start: 0.6711 (t0) cc_final: 0.6381 (p0) REVERT: N 311 HIS cc_start: 0.6031 (m90) cc_final: 0.5077 (t70) REVERT: N 384 LYS cc_start: 0.7635 (tmmt) cc_final: 0.7433 (tttp) REVERT: N 401 GLN cc_start: 0.7795 (tt0) cc_final: 0.6889 (mp10) REVERT: N 413 MET cc_start: 0.8806 (mtp) cc_final: 0.8534 (mtp) REVERT: N 453 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8037 (ttp-170) REVERT: N 490 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6938 (mpp-170) REVERT: N 606 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7204 (mt) REVERT: O 79 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7817 (mmt90) REVERT: P 12 ARG cc_start: 0.7833 (mtt180) cc_final: 0.7302 (mtm110) REVERT: P 49 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7305 (mmt-90) REVERT: Q 49 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7775 (mtp85) REVERT: R 57 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7634 (mt) REVERT: S 47 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6482 (tt0) REVERT: U 49 ARG cc_start: 0.8073 (mpt90) cc_final: 0.7430 (mmm160) REVERT: V 49 ARG cc_start: 0.8110 (mpt180) cc_final: 0.7775 (mmm160) REVERT: W 63 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8167 (mm-30) REVERT: W 79 ARG cc_start: 0.7323 (mtt-85) cc_final: 0.7083 (mtp85) REVERT: Z 47 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: M 30 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: M 59 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7393 (ttp80) REVERT: M 65 GLN cc_start: 0.8679 (mt0) cc_final: 0.8384 (mm-40) REVERT: M 67 LYS cc_start: 0.8311 (mtpm) cc_final: 0.7735 (ptpt) REVERT: M 71 ASP cc_start: 0.8334 (p0) cc_final: 0.7865 (p0) REVERT: M 111 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7928 (tt0) REVERT: M 171 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7217 (mtp180) REVERT: M 189 ARG cc_start: 0.7013 (ttm110) cc_final: 0.6538 (mmm-85) REVERT: M 220 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8164 (mttt) REVERT: M 301 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7720 (ttm-80) outliers start: 37 outliers final: 19 residues processed: 170 average time/residue: 1.7093 time to fit residues: 311.8001 Evaluate side-chains 174 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 153 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 179 optimal weight: 0.0370 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 183 HIS N 189 GLN M 26 GLN M 94 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109691 restraints weight = 14200.197| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.59 r_work: 0.3170 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.7867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14134 Z= 0.115 Angle : 0.483 8.316 19122 Z= 0.247 Chirality : 0.036 0.149 2258 Planarity : 0.005 0.052 2459 Dihedral : 4.429 80.275 2028 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.86 % Allowed : 18.42 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.20), residues: 1863 helix: 2.32 (0.14), residues: 1440 sheet: -1.15 (0.72), residues: 48 loop : -0.22 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 295 HIS 0.008 0.001 HIS N 183 PHE 0.011 0.001 PHE N 427 TYR 0.014 0.001 TYR N 43 ARG 0.009 0.000 ARG X 12 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 1114) hydrogen bonds : angle 3.45381 ( 3279) SS BOND : bond 0.00271 ( 1) SS BOND : angle 2.29454 ( 2) covalent geometry : bond 0.00236 (14133) covalent geometry : angle 0.48252 (19120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.7244 (mpt90) cc_final: 0.6631 (mtm110) REVERT: N 66 THR cc_start: 0.8743 (t) cc_final: 0.8467 (m) REVERT: N 120 GLU cc_start: 0.6701 (tt0) cc_final: 0.6300 (mp0) REVERT: N 155 GLU cc_start: 0.7034 (tt0) cc_final: 0.6261 (tm-30) REVERT: N 218 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7536 (mtm110) REVERT: N 306 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6896 (mm-30) REVERT: N 311 HIS cc_start: 0.5874 (m90) cc_final: 0.4990 (t70) REVERT: N 384 LYS cc_start: 0.7494 (tmmt) cc_final: 0.7258 (tttp) REVERT: N 401 GLN cc_start: 0.7398 (tt0) cc_final: 0.6646 (mp10) REVERT: N 453 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7949 (ttp-170) REVERT: N 490 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6841 (mpp-170) REVERT: N 606 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7104 (mt) REVERT: O 47 GLU cc_start: 0.7726 (tp30) cc_final: 0.7162 (tt0) REVERT: O 79 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7731 (mmt90) REVERT: P 12 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7213 (mtm110) REVERT: P 49 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7529 (ttm110) REVERT: Q 49 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7684 (mtp85) REVERT: U 49 ARG cc_start: 0.7995 (mpt90) cc_final: 0.7413 (mmm160) REVERT: V 49 ARG cc_start: 0.8123 (mpt180) cc_final: 0.7897 (tpp-160) REVERT: W 79 ARG cc_start: 0.7164 (mtt-85) cc_final: 0.6947 (mtp85) REVERT: Z 47 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: M 30 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7338 (m-30) REVERT: M 59 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7270 (ttp80) REVERT: M 65 GLN cc_start: 0.8545 (mt0) cc_final: 0.8225 (mm-40) REVERT: M 67 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7751 (ptpt) REVERT: M 71 ASP cc_start: 0.8257 (p0) cc_final: 0.7777 (p0) REVERT: M 111 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7939 (tt0) REVERT: M 171 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7182 (mtp180) REVERT: M 220 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8109 (mttt) REVERT: M 301 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7559 (ttm-80) outliers start: 25 outliers final: 12 residues processed: 168 average time/residue: 1.8623 time to fit residues: 336.2022 Evaluate side-chains 153 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 79 ARG Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 116 GLN N 183 HIS N 297 HIS N 338 ASN N 557 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102590 restraints weight = 14287.418| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.66 r_work: 0.3066 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14134 Z= 0.186 Angle : 0.585 8.226 19122 Z= 0.295 Chirality : 0.040 0.166 2258 Planarity : 0.005 0.058 2459 Dihedral : 4.623 80.662 2028 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.24 % Allowed : 18.12 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 1863 helix: 1.97 (0.13), residues: 1444 sheet: -1.31 (0.70), residues: 48 loop : -0.35 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 295 HIS 0.011 0.001 HIS N 183 PHE 0.017 0.001 PHE M 218 TYR 0.021 0.001 TYR N 43 ARG 0.010 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.06326 ( 1114) hydrogen bonds : angle 3.70977 ( 3279) SS BOND : bond 0.00891 ( 1) SS BOND : angle 3.05394 ( 2) covalent geometry : bond 0.00457 (14133) covalent geometry : angle 0.58465 (19120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12606.86 seconds wall clock time: 223 minutes 39.69 seconds (13419.69 seconds total)