Starting phenix.real_space_refine on Sun Jan 19 14:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywt_39644/01_2025/8ywt_39644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywt_39644/01_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_39644/01_2025/8ywt_39644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywt_39644/01_2025/8ywt_39644.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywt_39644/01_2025/8ywt_39644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywt_39644/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.67, per 1000 atoms: 0.62 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: 3.55 Conformation dependent library (CDL) restraints added in 2.1 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: 1.27 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: 4.44 Time building geometry restraints manager: 4.12 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.610 ------------------------------------------------------------------------------- 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 14133 Z= 0.826 Angle : 1.926 12.824 19120 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 *********************** 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 : 1.663 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: 1.2034 time to fit residues: 334.5955 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 : 1.483 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.160644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116727 restraints weight = 14633.644| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.76 r_work: 0.3363 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14133 Z= 0.247 Angle : 0.691 9.866 19120 Z= 0.350 Chirality : 0.043 0.178 2258 Planarity : 0.006 0.047 2459 Dihedral : 5.389 56.149 2050 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.88 % Allowed : 11.33 % Favored : 84.79 % 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: 1.12 (0.19), residues: 1863 helix: 0.96 (0.13), residues: 1435 sheet: -1.74 (0.71), residues: 47 loop : 0.68 (0.38), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 625 HIS 0.007 0.002 HIS N 491 PHE 0.016 0.002 PHE N 470 TYR 0.009 0.001 TYR N 165 ARG 0.009 0.001 ARG M 90 *********************** 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 228 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: N 120 GLU cc_start: 0.6390 (tt0) cc_final: 0.6101 (mp0) REVERT: N 155 GLU cc_start: 0.6644 (tt0) cc_final: 0.5814 (tm-30) REVERT: N 233 GLU cc_start: 0.7068 (tp30) cc_final: 0.6174 (tt0) REVERT: N 306 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6431 (mm-30) REVERT: N 401 GLN cc_start: 0.7039 (tt0) cc_final: 0.6431 (mp10) REVERT: N 413 MET cc_start: 0.8211 (mtp) cc_final: 0.7926 (mtp) REVERT: N 453 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7313 (ttp-170) REVERT: N 484 TYR cc_start: 0.7437 (t80) cc_final: 0.7233 (t80) REVERT: N 598 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6631 (mt) REVERT: N 606 LEU cc_start: 0.6773 (tt) cc_final: 0.6543 (mp) REVERT: N 627 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: N 638 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7909 (m-40) REVERT: P 12 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6704 (mtm110) REVERT: Q 12 ARG cc_start: 0.6998 (mtp180) cc_final: 0.6361 (mtp85) REVERT: X 12 ARG cc_start: 0.6970 (tpt170) cc_final: 0.6476 (mtp85) REVERT: M 21 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7304 (mttt) REVERT: M 85 ARG cc_start: 0.6344 (ttp80) cc_final: 0.6056 (ttt-90) REVERT: M 111 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7325 (tt0) REVERT: M 120 ARG cc_start: 0.7147 (mtt-85) cc_final: 0.6754 (mtt-85) REVERT: M 149 ARG cc_start: 0.6569 (ttm170) cc_final: 0.5740 (ttp80) REVERT: M 181 LYS cc_start: 0.6594 (ptpt) cc_final: 0.6351 (ptpt) REVERT: M 190 ASP cc_start: 0.6782 (t0) cc_final: 0.6124 (m-30) REVERT: M 205 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.5124 (t80) REVERT: M 220 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7515 (mptt) REVERT: M 291 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7343 (mmpt) outliers start: 52 outliers final: 7 residues processed: 218 average time/residue: 1.5839 time to fit residues: 372.6463 Evaluate side-chains 135 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 146 optimal weight: 0.5980 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: 2.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 V 51 ASN M 94 HIS M 145 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105848 restraints weight = 14876.107| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.65 r_work: 0.3195 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14133 Z= 0.285 Angle : 0.649 8.293 19120 Z= 0.326 Chirality : 0.041 0.161 2258 Planarity : 0.005 0.057 2459 Dihedral : 4.975 65.675 2032 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.47 % Allowed : 13.87 % Favored : 81.66 % 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: 1.70 (0.20), residues: 1863 helix: 1.48 (0.13), residues: 1432 sheet: -1.68 (0.77), residues: 43 loop : 0.39 (0.35), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 295 HIS 0.007 0.001 HIS N 557 PHE 0.017 0.002 PHE Z 68 TYR 0.015 0.002 TYR M 7 ARG 0.007 0.001 ARG M 90 *********************** 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 225 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 1.552 Fit side-chains REVERT: N 6 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: N 22 GLN cc_start: 0.6002 (mt0) cc_final: 0.5790 (mt0) REVERT: N 50 ARG cc_start: 0.6399 (mtt90) cc_final: 0.5724 (mtp180) REVERT: N 54 ARG cc_start: 0.6705 (mpt90) cc_final: 0.6086 (mtm110) REVERT: N 116 GLN cc_start: 0.7062 (pt0) cc_final: 0.6492 (mt0) REVERT: N 120 GLU cc_start: 0.6483 (tt0) cc_final: 0.6158 (mp0) REVERT: N 147 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7270 (mm-30) REVERT: N 155 GLU cc_start: 0.6740 (tt0) cc_final: 0.5956 (tm-30) REVERT: N 229 ARG cc_start: 0.6511 (mtm110) cc_final: 0.6285 (mtm-85) REVERT: N 233 GLU cc_start: 0.7203 (tp30) cc_final: 0.6252 (mt-10) REVERT: N 306 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6439 (mm-30) REVERT: N 311 HIS cc_start: 0.5371 (m90) cc_final: 0.4466 (t70) REVERT: N 344 THR cc_start: 0.7571 (m) cc_final: 0.7123 (p) REVERT: N 401 GLN cc_start: 0.7474 (tt0) cc_final: 0.6543 (mp10) REVERT: N 413 MET cc_start: 0.8274 (mtp) cc_final: 0.7985 (mtp) REVERT: N 453 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7756 (ttp-170) REVERT: N 484 TYR cc_start: 0.7843 (t80) cc_final: 0.7582 (t80) REVERT: N 492 MET cc_start: 0.8030 (mmm) cc_final: 0.7772 (mmt) REVERT: N 515 TYR cc_start: 0.5480 (m-80) cc_final: 0.5249 (m-80) REVERT: N 525 GLN cc_start: 0.7135 (tp40) cc_final: 0.6817 (tp40) REVERT: N 598 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6886 (mt) REVERT: N 606 LEU cc_start: 0.6810 (tt) cc_final: 0.6460 (mt) REVERT: O 47 GLU cc_start: 0.6996 (tp30) cc_final: 0.6246 (tt0) REVERT: P 12 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6739 (mtm110) REVERT: Q 12 ARG cc_start: 0.6882 (mtp180) cc_final: 0.6356 (mtp85) REVERT: S 63 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8282 (mm-30) REVERT: V 49 ARG cc_start: 0.7776 (mpt180) cc_final: 0.7381 (mmm160) REVERT: X 12 ARG cc_start: 0.6883 (tpt170) cc_final: 0.6483 (mtp85) REVERT: Z 12 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.5753 (ttp80) REVERT: Z 47 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: M 21 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7815 (mtmt) REVERT: M 59 ARG cc_start: 0.7244 (ttp-170) cc_final: 0.6763 (ttp-110) REVERT: M 67 LYS cc_start: 0.8007 (mtpm) cc_final: 0.7339 (mtmt) REVERT: M 71 ASP cc_start: 0.8073 (p0) cc_final: 0.7554 (p0) REVERT: M 111 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7466 (tt0) REVERT: M 220 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7564 (mttt) REVERT: M 227 ARG cc_start: 0.6692 (mtt-85) cc_final: 0.6367 (mtt-85) REVERT: M 301 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6668 (ttt90) outliers start: 60 outliers final: 18 residues processed: 207 average time/residue: 1.6868 time to fit residues: 375.4023 Evaluate side-chains 157 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 222 GLU Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 308 VAL Chi-restraints excluded: chain N residue 386 ASN 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 W residue 23 VAL 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 234 MET 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: 3.9990 chunk 100 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 65 HIS N 236 GLN N 605 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100738 restraints weight = 14850.796| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.70 r_work: 0.3145 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14133 Z= 0.356 Angle : 0.668 8.759 19120 Z= 0.334 Chirality : 0.043 0.177 2258 Planarity : 0.005 0.067 2459 Dihedral : 4.960 76.501 2028 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.00 % Allowed : 13.72 % Favored : 81.28 % 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: 1.54 (0.19), residues: 1863 helix: 1.44 (0.13), residues: 1433 sheet: -1.90 (0.67), residues: 48 loop : 0.07 (0.34), residues: 382 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 0.008 0.001 ARG R 79 *********************** 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 221 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6866 (mpt90) cc_final: 0.6113 (mtm110) REVERT: N 120 GLU cc_start: 0.6681 (tt0) cc_final: 0.6250 (mp0) REVERT: N 147 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7343 (mm-30) REVERT: N 155 GLU cc_start: 0.6552 (tt0) cc_final: 0.5884 (tm-30) REVERT: N 159 LYS cc_start: 0.6878 (mtmt) cc_final: 0.6503 (tptt) REVERT: N 215 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6449 (tm-30) REVERT: N 229 ARG cc_start: 0.6710 (mtm110) cc_final: 0.6419 (mtm-85) REVERT: N 233 GLU cc_start: 0.7097 (tp30) cc_final: 0.6339 (mt-10) REVERT: N 306 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6632 (mm-30) REVERT: N 311 HIS cc_start: 0.5816 (m90) cc_final: 0.4728 (t70) REVERT: N 344 THR cc_start: 0.7675 (m) cc_final: 0.7249 (p) REVERT: N 397 LYS cc_start: 0.7477 (tttt) cc_final: 0.7223 (tmtt) REVERT: N 401 GLN cc_start: 0.7669 (tt0) cc_final: 0.6645 (mp10) REVERT: N 413 MET cc_start: 0.8452 (mtp) cc_final: 0.8194 (mtp) REVERT: N 453 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7805 (ttp-170) REVERT: N 484 TYR cc_start: 0.7771 (t80) cc_final: 0.7536 (t80) REVERT: N 490 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6673 (mpp-170) REVERT: N 492 MET cc_start: 0.8047 (mmm) cc_final: 0.7820 (mmt) REVERT: N 516 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6270 (mp) REVERT: N 525 GLN cc_start: 0.7180 (tp40) cc_final: 0.6900 (tp40) REVERT: N 598 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6983 (mt) REVERT: N 606 LEU cc_start: 0.7024 (tt) cc_final: 0.6637 (mt) REVERT: P 12 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6601 (mtm110) REVERT: Q 12 ARG cc_start: 0.6880 (mtp180) cc_final: 0.6283 (mtp85) REVERT: S 47 GLU cc_start: 0.6230 (mt-10) cc_final: 0.5704 (tt0) REVERT: U 49 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6975 (mmm160) REVERT: V 49 ARG cc_start: 0.7866 (mpt180) cc_final: 0.7443 (mmm160) REVERT: X 12 ARG cc_start: 0.6955 (tpt170) cc_final: 0.6674 (mtp85) REVERT: Z 47 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: M 59 ARG cc_start: 0.7319 (ttp-170) cc_final: 0.6675 (ttp80) REVERT: M 71 ASP cc_start: 0.8126 (p0) cc_final: 0.7645 (p0) REVERT: M 111 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7549 (tt0) REVERT: M 171 ARG cc_start: 0.7367 (mtt90) cc_final: 0.6555 (mtp180) REVERT: M 190 ASP cc_start: 0.6746 (t0) cc_final: 0.6475 (m-30) REVERT: M 220 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7572 (mttt) REVERT: M 301 ARG cc_start: 0.7421 (mmm160) cc_final: 0.6731 (ttt90) outliers start: 67 outliers final: 31 residues processed: 200 average time/residue: 1.5475 time to fit residues: 334.8866 Evaluate side-chains 176 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 180 VAL 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 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 490 ARG Chi-restraints excluded: chain N residue 516 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 O residue 54 THR 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 Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 605 HIS M 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104181 restraints weight = 14914.283| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.72 r_work: 0.3198 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14133 Z= 0.199 Angle : 0.536 8.478 19120 Z= 0.273 Chirality : 0.038 0.144 2258 Planarity : 0.005 0.063 2459 Dihedral : 4.707 77.285 2028 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.65 % Allowed : 15.06 % Favored : 81.28 % 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: 2.04 (0.19), residues: 1863 helix: 1.85 (0.13), residues: 1441 sheet: -2.00 (0.66), residues: 48 loop : 0.01 (0.33), residues: 374 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 0.020 0.001 PHE N 427 TYR 0.016 0.001 TYR N 43 ARG 0.008 0.000 ARG R 79 *********************** 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 204 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: N 50 ARG cc_start: 0.6463 (mtt90) cc_final: 0.5846 (mtp85) REVERT: N 54 ARG cc_start: 0.6757 (mpt90) cc_final: 0.6078 (mtm110) REVERT: N 66 THR cc_start: 0.8413 (t) cc_final: 0.8078 (m) REVERT: N 75 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: N 120 GLU cc_start: 0.6627 (tt0) cc_final: 0.6193 (mp0) REVERT: N 147 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7268 (mm-30) REVERT: N 155 GLU cc_start: 0.6560 (tt0) cc_final: 0.5904 (tm-30) REVERT: N 159 LYS cc_start: 0.6835 (mtmt) cc_final: 0.6579 (tmtm) REVERT: N 229 ARG cc_start: 0.6657 (mtm110) cc_final: 0.6217 (mtt180) REVERT: N 233 GLU cc_start: 0.7075 (tp30) cc_final: 0.6324 (mt-10) REVERT: N 306 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6560 (mm-30) REVERT: N 311 HIS cc_start: 0.5526 (m90) cc_final: 0.4490 (t70) REVERT: N 397 LYS cc_start: 0.7473 (tttt) cc_final: 0.7223 (tmtt) REVERT: N 401 GLN cc_start: 0.7490 (tt0) cc_final: 0.6527 (mp10) REVERT: N 413 MET cc_start: 0.8263 (mtp) cc_final: 0.8011 (mtp) REVERT: N 446 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7660 (mp) REVERT: N 453 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7744 (ttp-170) REVERT: N 484 TYR cc_start: 0.7719 (t80) cc_final: 0.7486 (t80) REVERT: N 492 MET cc_start: 0.8020 (mmm) cc_final: 0.7803 (mmt) REVERT: N 525 GLN cc_start: 0.7068 (tp40) cc_final: 0.6819 (tp40) REVERT: N 598 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6839 (mt) REVERT: N 606 LEU cc_start: 0.6969 (tt) cc_final: 0.6613 (mt) REVERT: O 47 GLU cc_start: 0.7209 (tp30) cc_final: 0.6478 (tt0) REVERT: O 79 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7282 (mmt90) REVERT: P 12 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6508 (mtm110) REVERT: S 47 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5776 (tt0) REVERT: V 49 ARG cc_start: 0.7852 (mpt180) cc_final: 0.7429 (mmm160) REVERT: W 79 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.6534 (mtp85) REVERT: X 12 ARG cc_start: 0.6922 (tpt170) cc_final: 0.6552 (mtp85) REVERT: X 64 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7657 (p) REVERT: Y 47 GLU cc_start: 0.7879 (tp30) cc_final: 0.7483 (tp30) REVERT: Z 47 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: M 59 ARG cc_start: 0.7262 (ttp-170) cc_final: 0.6655 (ttp-110) REVERT: M 65 GLN cc_start: 0.8369 (mt0) cc_final: 0.8057 (mm-40) REVERT: M 71 ASP cc_start: 0.8072 (p0) cc_final: 0.7561 (p0) REVERT: M 111 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7547 (tt0) REVERT: M 171 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6436 (mtp180) REVERT: M 220 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7562 (mttt) REVERT: M 301 ARG cc_start: 0.7347 (mmm160) cc_final: 0.7006 (ttm-80) outliers start: 49 outliers final: 21 residues processed: 182 average time/residue: 1.5556 time to fit residues: 306.3942 Evaluate side-chains 172 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 75 GLU Chi-restraints excluded: chain N residue 122 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 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 528 MET 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 P residue 11 ASP Chi-restraints excluded: chain U residue 47 GLU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 chunk 52 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 26 GLN M 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104908 restraints weight = 14854.382| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.71 r_work: 0.3207 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14133 Z= 0.188 Angle : 0.513 8.051 19120 Z= 0.261 Chirality : 0.037 0.150 2258 Planarity : 0.005 0.056 2459 Dihedral : 4.563 78.477 2028 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.65 % Allowed : 14.69 % Favored : 81.66 % 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: 2.37 (0.20), residues: 1863 helix: 2.10 (0.14), residues: 1442 sheet: -1.59 (0.69), residues: 48 loop : -0.01 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 295 HIS 0.003 0.001 HIS N 557 PHE 0.014 0.001 PHE N 427 TYR 0.015 0.001 TYR M 7 ARG 0.008 0.000 ARG R 79 *********************** 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 199 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: N 36 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.6939 (mtm-85) REVERT: N 54 ARG cc_start: 0.6743 (mpt90) cc_final: 0.6109 (mtm110) REVERT: N 66 THR cc_start: 0.8452 (t) cc_final: 0.8110 (m) REVERT: N 75 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7157 (pt0) REVERT: N 120 GLU cc_start: 0.6461 (tt0) cc_final: 0.6052 (mp0) REVERT: N 147 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7268 (mm-30) REVERT: N 155 GLU cc_start: 0.6598 (tt0) cc_final: 0.5921 (tm-30) REVERT: N 188 ASP cc_start: 0.6071 (m-30) cc_final: 0.5864 (m-30) REVERT: N 229 ARG cc_start: 0.6607 (mtm110) cc_final: 0.6365 (mtt180) REVERT: N 237 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6831 (m-70) REVERT: N 306 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6498 (mm-30) REVERT: N 311 HIS cc_start: 0.5515 (m90) cc_final: 0.4486 (t70) REVERT: N 397 LYS cc_start: 0.7555 (tttt) cc_final: 0.7244 (tmtt) REVERT: N 401 GLN cc_start: 0.7385 (tt0) cc_final: 0.6393 (mp10) REVERT: N 413 MET cc_start: 0.8273 (mtp) cc_final: 0.8018 (mtp) REVERT: N 446 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7738 (mp) REVERT: N 453 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7616 (ttp-170) REVERT: N 484 TYR cc_start: 0.7718 (t80) cc_final: 0.7511 (t80) REVERT: N 492 MET cc_start: 0.8106 (mmm) cc_final: 0.7797 (mmt) REVERT: N 525 GLN cc_start: 0.7051 (tp40) cc_final: 0.6830 (tp40) REVERT: N 543 ARG cc_start: 0.7018 (mtp85) cc_final: 0.6780 (mtp85) REVERT: N 598 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6833 (mt) REVERT: N 606 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6635 (mt) REVERT: O 47 GLU cc_start: 0.7219 (tp30) cc_final: 0.6507 (tt0) REVERT: O 79 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7287 (mmt90) REVERT: P 12 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6451 (mtm110) REVERT: U 79 ARG cc_start: 0.7267 (mmt180) cc_final: 0.7004 (mtt-85) REVERT: V 49 ARG cc_start: 0.7825 (mpt180) cc_final: 0.7425 (mmm160) REVERT: W 79 ARG cc_start: 0.6975 (mtt-85) cc_final: 0.6520 (mtp85) REVERT: X 12 ARG cc_start: 0.6983 (tpt170) cc_final: 0.6651 (mtp85) REVERT: X 64 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7665 (p) REVERT: Z 47 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: M 30 ASP cc_start: 0.7448 (p0) cc_final: 0.7094 (m-30) REVERT: M 59 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6656 (ttp-110) REVERT: M 67 LYS cc_start: 0.7873 (mtpm) cc_final: 0.7225 (ptpt) REVERT: M 71 ASP cc_start: 0.8102 (p0) cc_final: 0.7605 (p0) REVERT: M 111 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7584 (tt0) REVERT: M 220 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7623 (mttt) REVERT: M 301 ARG cc_start: 0.7315 (mmm160) cc_final: 0.6947 (ttm-80) outliers start: 49 outliers final: 17 residues processed: 179 average time/residue: 1.6641 time to fit residues: 320.2747 Evaluate side-chains 163 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 122 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 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 528 MET Chi-restraints excluded: chain N residue 598 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 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 Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 182 optimal weight: 0.0770 chunk 32 optimal weight: 0.2980 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101209 restraints weight = 14983.096| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.69 r_work: 0.3157 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.7554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14133 Z= 0.262 Angle : 0.570 7.496 19120 Z= 0.288 Chirality : 0.039 0.161 2258 Planarity : 0.005 0.060 2459 Dihedral : 4.683 79.796 2028 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.50 % Allowed : 15.73 % 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: 2.14 (0.19), residues: 1863 helix: 1.96 (0.13), residues: 1436 sheet: -1.62 (0.69), residues: 48 loop : -0.19 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 295 HIS 0.004 0.001 HIS N 557 PHE 0.017 0.001 PHE M 172 TYR 0.018 0.001 TYR N 43 ARG 0.011 0.000 ARG N 218 *********************** 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 194 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.6878 (mtm-85) REVERT: N 54 ARG cc_start: 0.6845 (mpt90) cc_final: 0.6171 (mtm110) REVERT: N 66 THR cc_start: 0.8489 (t) cc_final: 0.8096 (m) REVERT: N 75 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7125 (pt0) REVERT: N 120 GLU cc_start: 0.6533 (tt0) cc_final: 0.6116 (mp0) REVERT: N 147 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7268 (mm-30) REVERT: N 155 GLU cc_start: 0.6677 (tt0) cc_final: 0.5880 (tm-30) REVERT: N 229 ARG cc_start: 0.6580 (mtm110) cc_final: 0.6322 (mtt180) REVERT: N 237 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6868 (m-70) REVERT: N 306 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6260 (tt0) REVERT: N 311 HIS cc_start: 0.5616 (m90) cc_final: 0.4568 (t70) REVERT: N 384 LYS cc_start: 0.7245 (tmmt) cc_final: 0.6985 (tttp) REVERT: N 401 GLN cc_start: 0.7546 (tt0) cc_final: 0.6505 (mp10) REVERT: N 413 MET cc_start: 0.8411 (mtp) cc_final: 0.8118 (mtp) REVERT: N 446 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7671 (mp) REVERT: N 453 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7694 (ttp-170) REVERT: N 484 TYR cc_start: 0.7782 (t80) cc_final: 0.7563 (t80) REVERT: N 492 MET cc_start: 0.8020 (mmm) cc_final: 0.7818 (mmt) REVERT: N 525 GLN cc_start: 0.7064 (tp40) cc_final: 0.6761 (tp40) REVERT: N 606 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6640 (mt) REVERT: O 79 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7244 (mmt90) REVERT: P 12 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6539 (mtm110) REVERT: Q 49 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7470 (mtp85) REVERT: R 49 ARG cc_start: 0.7607 (mpt180) cc_final: 0.7145 (mmm160) REVERT: S 47 GLU cc_start: 0.6381 (mt-10) cc_final: 0.5838 (tt0) REVERT: U 49 ARG cc_start: 0.7754 (mpt180) cc_final: 0.6980 (mmm160) REVERT: U 79 ARG cc_start: 0.7217 (mmt180) cc_final: 0.6957 (mtt-85) REVERT: V 49 ARG cc_start: 0.7879 (mpt180) cc_final: 0.7447 (mmm160) REVERT: W 63 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7829 (mm-30) REVERT: W 79 ARG cc_start: 0.6954 (mtt-85) cc_final: 0.6599 (mtp85) REVERT: X 12 ARG cc_start: 0.6938 (tpt170) cc_final: 0.6586 (mtp85) REVERT: Z 47 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: M 30 ASP cc_start: 0.7522 (p0) cc_final: 0.7138 (m-30) REVERT: M 59 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6629 (ttp80) REVERT: M 67 LYS cc_start: 0.7904 (mtpm) cc_final: 0.7212 (ptpt) REVERT: M 71 ASP cc_start: 0.8181 (p0) cc_final: 0.7686 (p0) REVERT: M 85 ARG cc_start: 0.6933 (ttp80) cc_final: 0.6576 (ttt-90) REVERT: M 111 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7542 (tt0) REVERT: M 220 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7628 (mttt) REVERT: M 301 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6983 (ttm-80) REVERT: M 306 ARG cc_start: 0.7179 (tmm160) cc_final: 0.6948 (ttp80) outliers start: 47 outliers final: 19 residues processed: 175 average time/residue: 1.7621 time to fit residues: 331.7163 Evaluate side-chains 168 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 220 LEU 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 490 ARG Chi-restraints excluded: chain N residue 528 MET 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 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 59 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 90 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 26 GLN M 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109290 restraints weight = 14230.597| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.68 r_work: 0.3154 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.7676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14133 Z= 0.159 Angle : 0.486 8.172 19120 Z= 0.250 Chirality : 0.036 0.149 2258 Planarity : 0.004 0.052 2459 Dihedral : 4.489 79.797 2028 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.86 % Allowed : 17.52 % Favored : 80.61 % 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: 2.59 (0.20), residues: 1863 helix: 2.29 (0.14), residues: 1440 sheet: -1.42 (0.71), residues: 48 loop : -0.10 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.004 0.001 HIS M 94 PHE 0.013 0.001 PHE M 172 TYR 0.014 0.001 TYR M 7 ARG 0.009 0.000 ARG N 218 *********************** 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 174 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: N 36 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7295 (mtm-85) REVERT: N 54 ARG cc_start: 0.7313 (mpt90) cc_final: 0.6668 (mtm110) REVERT: N 66 THR cc_start: 0.8750 (t) cc_final: 0.8426 (m) REVERT: N 120 GLU cc_start: 0.6729 (tt0) cc_final: 0.6356 (mp0) REVERT: N 147 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7517 (mm-30) REVERT: N 155 GLU cc_start: 0.6932 (tt0) cc_final: 0.6165 (tm-30) REVERT: N 237 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.7207 (m-70) REVERT: N 306 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6709 (tt0) REVERT: N 311 HIS cc_start: 0.5551 (m90) cc_final: 0.4666 (t70) REVERT: N 384 LYS cc_start: 0.7502 (tmmt) cc_final: 0.7284 (tttp) REVERT: N 401 GLN cc_start: 0.7491 (tt0) cc_final: 0.6718 (mp10) REVERT: N 413 MET cc_start: 0.8662 (mtp) cc_final: 0.8442 (mtp) REVERT: N 446 LEU cc_start: 0.8454 (tp) cc_final: 0.7996 (mt) REVERT: N 453 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7912 (ttp-170) REVERT: N 525 GLN cc_start: 0.7401 (tp40) cc_final: 0.7147 (tp40) REVERT: N 606 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7141 (mt) REVERT: O 47 GLU cc_start: 0.7604 (tp30) cc_final: 0.6982 (tt0) REVERT: O 79 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7765 (mmt90) REVERT: P 12 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7193 (mtm110) REVERT: Q 49 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7696 (mtp85) REVERT: R 49 ARG cc_start: 0.7665 (mpt180) cc_final: 0.7372 (mmm160) REVERT: U 49 ARG cc_start: 0.8000 (mpt180) cc_final: 0.7370 (mmm160) REVERT: U 79 ARG cc_start: 0.7534 (mmt180) cc_final: 0.7331 (mtt-85) REVERT: V 49 ARG cc_start: 0.8113 (mpt180) cc_final: 0.7739 (mmm160) REVERT: W 79 ARG cc_start: 0.7246 (mtt-85) cc_final: 0.6970 (mtp85) REVERT: Z 47 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: M 30 ASP cc_start: 0.7592 (p0) cc_final: 0.7220 (m-30) REVERT: M 59 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7322 (ttp80) REVERT: M 67 LYS cc_start: 0.8212 (mtpm) cc_final: 0.7736 (ptpt) REVERT: M 71 ASP cc_start: 0.8267 (p0) cc_final: 0.7782 (p0) REVERT: M 111 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7935 (tt0) REVERT: M 220 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8007 (mttt) REVERT: M 301 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7564 (ttm-80) outliers start: 25 outliers final: 10 residues processed: 163 average time/residue: 1.7897 time to fit residues: 313.4153 Evaluate side-chains 152 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 237 HIS Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 1.9990 chunk 162 optimal weight: 0.0870 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: 4.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 116 GLN N 338 ASN M 26 GLN M 94 HIS M 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106139 restraints weight = 14128.307| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.67 r_work: 0.3112 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14133 Z= 0.206 Angle : 0.524 8.121 19120 Z= 0.266 Chirality : 0.038 0.153 2258 Planarity : 0.005 0.054 2459 Dihedral : 4.503 80.181 2028 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.54 % Allowed : 17.23 % Favored : 80.24 % 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 (0.13), residues: 1439 sheet: -1.44 (0.72), residues: 48 loop : -0.17 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 295 HIS 0.003 0.001 HIS N 557 PHE 0.014 0.001 PHE M 172 TYR 0.016 0.001 TYR M 7 ARG 0.008 0.000 ARG R 79 *********************** 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 177 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: N 36 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7171 (mtm-85) REVERT: N 54 ARG cc_start: 0.7277 (mpt90) cc_final: 0.6669 (mtm110) REVERT: N 66 THR cc_start: 0.8759 (t) cc_final: 0.8395 (m) REVERT: N 120 GLU cc_start: 0.6742 (tt0) cc_final: 0.6362 (mp0) REVERT: N 147 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7488 (mm-30) REVERT: N 155 GLU cc_start: 0.6974 (tt0) cc_final: 0.6202 (tm-30) REVERT: N 184 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6642 (ttp-110) REVERT: N 306 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6789 (tt0) REVERT: N 311 HIS cc_start: 0.5689 (m90) cc_final: 0.4656 (t70) REVERT: N 384 LYS cc_start: 0.7528 (tmmt) cc_final: 0.7314 (tttp) REVERT: N 401 GLN cc_start: 0.7632 (tt0) cc_final: 0.6753 (mp10) REVERT: N 413 MET cc_start: 0.8738 (mtp) cc_final: 0.8454 (mtp) REVERT: N 453 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8006 (ttp-170) REVERT: N 490 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6906 (mpp-170) REVERT: N 606 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7162 (mt) REVERT: O 47 GLU cc_start: 0.7671 (tp30) cc_final: 0.7041 (tt0) REVERT: O 79 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7763 (mmt90) REVERT: P 12 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7202 (mtm110) REVERT: P 49 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7170 (mmt-90) REVERT: Q 49 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7712 (mtp85) REVERT: R 49 ARG cc_start: 0.7623 (mpt180) cc_final: 0.7331 (mmm160) REVERT: U 49 ARG cc_start: 0.7958 (mpt180) cc_final: 0.7374 (mmm160) REVERT: U 79 ARG cc_start: 0.7627 (mmt180) cc_final: 0.7412 (mtt-85) REVERT: V 49 ARG cc_start: 0.8095 (mpt180) cc_final: 0.7731 (mmm160) REVERT: W 79 ARG cc_start: 0.7274 (mtt-85) cc_final: 0.7039 (mtp85) REVERT: Z 47 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: M 30 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: M 59 ARG cc_start: 0.7738 (ttp-170) cc_final: 0.7265 (ttp80) REVERT: M 65 GLN cc_start: 0.8619 (mt0) cc_final: 0.8348 (mm-40) REVERT: M 67 LYS cc_start: 0.8255 (mtpm) cc_final: 0.7724 (ptpt) REVERT: M 71 ASP cc_start: 0.8318 (p0) cc_final: 0.7829 (p0) REVERT: M 111 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7935 (tt0) REVERT: M 220 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8021 (mttt) REVERT: M 301 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7623 (ttm-80) outliers start: 34 outliers final: 15 residues processed: 163 average time/residue: 1.7533 time to fit residues: 307.2202 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 : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 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 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 54 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 61 optimal weight: 0.0030 chunk 31 optimal weight: 0.0570 chunk 124 optimal weight: 6.9990 chunk 179 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 overall best weight: 0.4508 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.154283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110434 restraints weight = 14155.690| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.60 r_work: 0.3173 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.7783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14133 Z= 0.157 Angle : 0.484 8.302 19120 Z= 0.248 Chirality : 0.036 0.155 2258 Planarity : 0.005 0.050 2459 Dihedral : 4.394 80.102 2028 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.86 % Allowed : 18.12 % Favored : 80.01 % 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: 2.74 (0.20), residues: 1863 helix: 2.42 (0.14), residues: 1440 sheet: -1.33 (0.72), residues: 48 loop : -0.15 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.003 0.000 HIS M 94 PHE 0.012 0.001 PHE M 172 TYR 0.014 0.001 TYR M 7 ARG 0.008 0.000 ARG X 12 ********************** 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 175 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: N 36 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.6987 (mtm-85) REVERT: N 54 ARG cc_start: 0.7247 (mpt90) cc_final: 0.6629 (mtm110) REVERT: N 66 THR cc_start: 0.8741 (t) cc_final: 0.8413 (m) REVERT: N 120 GLU cc_start: 0.6667 (tt0) cc_final: 0.6326 (mp0) REVERT: N 147 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7470 (mm-30) REVERT: N 155 GLU cc_start: 0.7021 (tt0) cc_final: 0.6247 (tm-30) REVERT: N 306 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6792 (tt0) REVERT: N 311 HIS cc_start: 0.5496 (m90) cc_final: 0.4490 (t70) REVERT: N 384 LYS cc_start: 0.7495 (tmmt) cc_final: 0.7258 (tttp) REVERT: N 401 GLN cc_start: 0.7395 (tt0) cc_final: 0.6649 (mp10) REVERT: N 453 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7951 (ttp-170) REVERT: N 490 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6875 (mpp-170) REVERT: N 606 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7138 (mt) REVERT: O 47 GLU cc_start: 0.7619 (tp30) cc_final: 0.7005 (tt0) REVERT: P 12 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7169 (mtm110) REVERT: P 49 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7139 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7680 (mtp85) REVERT: R 49 ARG cc_start: 0.7537 (mpt180) cc_final: 0.7264 (mmm160) REVERT: U 49 ARG cc_start: 0.7925 (mpt180) cc_final: 0.7382 (mmm160) REVERT: V 49 ARG cc_start: 0.8134 (mpt180) cc_final: 0.7927 (tpp-160) REVERT: W 63 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8072 (mm-30) REVERT: W 79 ARG cc_start: 0.7059 (mtt-85) cc_final: 0.6856 (mtp85) REVERT: Z 47 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: M 30 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: M 59 ARG cc_start: 0.7746 (ttp-170) cc_final: 0.7288 (ttp80) REVERT: M 65 GLN cc_start: 0.8522 (mt0) cc_final: 0.8279 (mm-40) REVERT: M 67 LYS cc_start: 0.8216 (mtpm) cc_final: 0.7787 (ptpt) REVERT: M 71 ASP cc_start: 0.8264 (p0) cc_final: 0.7768 (p0) REVERT: M 111 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7896 (tt0) REVERT: M 220 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8025 (mttt) REVERT: M 301 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7538 (ttm-80) outliers start: 25 outliers final: 12 residues processed: 165 average time/residue: 1.8783 time to fit residues: 333.9487 Evaluate side-chains 156 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 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 V residue 66 VAL Chi-restraints excluded: chain V residue 67 ILE 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 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: 0.1980 chunk 116 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 297 HIS N 338 ASN N 557 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101564 restraints weight = 14279.851| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.66 r_work: 0.3045 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.7762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14133 Z= 0.360 Angle : 0.639 8.127 19120 Z= 0.321 Chirality : 0.043 0.170 2258 Planarity : 0.005 0.058 2459 Dihedral : 4.727 81.050 2028 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.01 % Allowed : 17.75 % Favored : 80.24 % 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: 2.00 (0.19), residues: 1863 helix: 1.88 (0.13), residues: 1444 sheet: -1.62 (0.69), residues: 48 loop : -0.38 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP N 56 HIS 0.006 0.001 HIS N 557 PHE 0.019 0.002 PHE M 218 TYR 0.022 0.002 TYR N 43 ARG 0.009 0.001 ARG X 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10299.62 seconds wall clock time: 183 minutes 38.63 seconds (11018.63 seconds total)