Starting phenix.real_space_refine on Thu Sep 18 03:56:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywt_39644/09_2025/8ywt_39644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywt_39644/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ywt_39644/09_2025/8ywt_39644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywt_39644/09_2025/8ywt_39644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ywt_39644/09_2025/8ywt_39644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywt_39644/09_2025/8ywt_39644.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'GLN:plan1': 1, '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: {'GLU:plan': 4, 'GLN:plan1': 3} 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: 3.49, per 1000 atoms: 0.25 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: 0.87 Conformation dependent library (CDL) restraints added in 640.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.33 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: 2.35 Time building geometry restraints manager: 1.15 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: 2.190 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.103 14134 Z= 0.815 Angle : 1.926 12.824 19122 Z= 1.327 Chirality : 0.091 0.432 2258 Planarity : 0.019 0.303 2459 Dihedral : 14.343 86.972 5007 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.09 % Favored : 97.64 % Rotamer: Outliers : 3.36 % Allowed : 6.64 % Favored : 90.01 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG M 266 TYR 0.150 0.024 TYR N 118 PHE 0.070 0.013 PHE X 68 TRP 0.068 0.019 TRP N 545 HIS 0.013 0.004 HIS N 297 Details of bonding type rmsd covalent geometry : bond 0.01260 (14133) covalent geometry : angle 1.92554 (19120) SS BOND : bond 0.02114 ( 1) SS BOND : angle 2.57436 ( 2) hydrogen bonds : bond 0.22015 ( 1114) hydrogen bonds : angle 7.07015 ( 3279) *********************** 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 : 0.527 Fit side-chains REVERT: N 155 GLU cc_start: 0.6652 (tt0) cc_final: 0.5828 (tm-30) REVERT: N 306 GLU cc_start: 0.6246 (mt-10) cc_final: 0.6040 (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: 0.5686 time to fit residues: 157.5084 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 : 0.421 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.160212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117653 restraints weight = 14639.742| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.71 r_work: 0.3367 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14134 Z= 0.186 Angle : 0.671 8.627 19122 Z= 0.347 Chirality : 0.042 0.201 2258 Planarity : 0.006 0.048 2459 Dihedral : 5.364 55.091 2050 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.80 % Allowed : 11.26 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1863 helix: 1.02 (0.13), residues: 1431 sheet: -1.70 (0.72), residues: 47 loop : 0.66 (0.38), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 90 TYR 0.010 0.001 TYR N 281 PHE 0.015 0.002 PHE M 172 TRP 0.012 0.001 TRP N 420 HIS 0.006 0.002 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00367 (14133) covalent geometry : angle 0.67087 (19120) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.56481 ( 2) hydrogen bonds : bond 0.06006 ( 1114) hydrogen bonds : angle 4.00902 ( 3279) *********************** 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 224 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: N 120 GLU cc_start: 0.6373 (tt0) cc_final: 0.6088 (mp0) REVERT: N 155 GLU cc_start: 0.6624 (tt0) cc_final: 0.5780 (tm-30) REVERT: N 233 GLU cc_start: 0.7068 (tp30) cc_final: 0.6168 (tt0) REVERT: N 306 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6419 (mm-30) REVERT: N 401 GLN cc_start: 0.7029 (tt0) cc_final: 0.6432 (mp10) REVERT: N 413 MET cc_start: 0.8184 (mtp) cc_final: 0.7807 (mtp) REVERT: N 453 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7276 (ttp-170) REVERT: N 598 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6646 (mt) REVERT: N 606 LEU cc_start: 0.6710 (tt) cc_final: 0.6474 (mp) REVERT: N 627 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: N 638 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7833 (m-40) REVERT: P 12 ARG cc_start: 0.7081 (mtt180) cc_final: 0.6677 (mtm110) REVERT: Q 12 ARG cc_start: 0.6949 (mtp180) cc_final: 0.6349 (mtp85) REVERT: S 63 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8126 (mm-30) REVERT: X 12 ARG cc_start: 0.6906 (tpt170) cc_final: 0.6500 (mtp85) REVERT: M 85 ARG cc_start: 0.6277 (ttp80) cc_final: 0.6012 (ttt-90) REVERT: M 111 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7289 (tt0) REVERT: M 120 ARG cc_start: 0.7128 (mtt-85) cc_final: 0.6720 (mtt-85) REVERT: M 149 ARG cc_start: 0.6522 (ttm170) cc_final: 0.5714 (ttp80) REVERT: M 181 LYS cc_start: 0.6567 (ptpt) cc_final: 0.6331 (ptpt) REVERT: M 205 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.5117 (t80) REVERT: M 220 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7498 (mptt) REVERT: M 291 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7324 (mmpt) outliers start: 51 outliers final: 8 residues processed: 216 average time/residue: 0.7475 time to fit residues: 173.7201 Evaluate side-chains 130 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 308 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 627 GLU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain M residue 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 60 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 N 408 HIS 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 = 0.3951 r_free = 0.3951 target = 0.164643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125968 restraints weight = 15308.176| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.53 r_work: 0.3469 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14134 Z= 0.152 Angle : 0.582 8.369 19122 Z= 0.298 Chirality : 0.039 0.153 2258 Planarity : 0.005 0.088 2459 Dihedral : 4.792 66.578 2032 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.80 % Allowed : 14.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.20), residues: 1863 helix: 1.73 (0.13), residues: 1434 sheet: -1.62 (0.76), residues: 45 loop : 0.48 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 184 TYR 0.016 0.001 TYR M 7 PHE 0.015 0.001 PHE M 172 TRP 0.010 0.001 TRP M 295 HIS 0.006 0.001 HIS N 557 Details of bonding type rmsd covalent geometry : bond 0.00323 (14133) covalent geometry : angle 0.58153 (19120) SS BOND : bond 0.00411 ( 1) SS BOND : angle 1.83751 ( 2) hydrogen bonds : bond 0.06157 ( 1114) hydrogen bonds : angle 3.78428 ( 3279) *********************** 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 218 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 0.555 Fit side-chains REVERT: N 22 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.5807 (mp10) REVERT: N 50 ARG cc_start: 0.6812 (mtt90) cc_final: 0.6226 (mtp180) REVERT: N 116 GLN cc_start: 0.7494 (pt0) cc_final: 0.7059 (mt0) REVERT: N 155 GLU cc_start: 0.7040 (tt0) cc_final: 0.6241 (tm-30) REVERT: N 233 GLU cc_start: 0.7509 (tp30) cc_final: 0.6723 (mt-10) REVERT: N 306 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6981 (mm-30) REVERT: N 311 HIS cc_start: 0.5296 (m90) cc_final: 0.4507 (t70) REVERT: N 401 GLN cc_start: 0.7619 (tt0) cc_final: 0.6893 (mp10) REVERT: N 446 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7889 (mt) REVERT: N 453 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8076 (ttp-170) REVERT: N 525 GLN cc_start: 0.7649 (tp40) cc_final: 0.7300 (tp40) REVERT: N 598 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7372 (mt) REVERT: N 606 LEU cc_start: 0.7477 (tt) cc_final: 0.7078 (mt) REVERT: N 638 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8318 (m-40) REVERT: O 47 GLU cc_start: 0.7266 (tp30) cc_final: 0.6678 (tt0) REVERT: P 12 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7412 (mtm110) REVERT: S 47 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6378 (tt0) REVERT: V 49 ARG cc_start: 0.7770 (mpt180) cc_final: 0.7525 (mmm160) REVERT: Z 47 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: M 59 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7350 (ttp-110) REVERT: M 67 LYS cc_start: 0.8482 (mtpm) cc_final: 0.7694 (ptpt) REVERT: M 71 ASP cc_start: 0.8156 (p0) cc_final: 0.7651 (p0) REVERT: M 111 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7731 (tt0) REVERT: M 190 ASP cc_start: 0.7077 (t0) cc_final: 0.6769 (m-30) REVERT: M 220 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7955 (mttt) outliers start: 51 outliers final: 11 residues processed: 202 average time/residue: 0.7673 time to fit residues: 166.7277 Evaluate side-chains 145 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain 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 159 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 182 optimal weight: 0.0670 chunk 113 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 65 HIS N 605 HIS N 616 HIS V 51 ASN M 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105212 restraints weight = 14915.226| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.71 r_work: 0.3209 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14134 Z= 0.151 Angle : 0.563 8.147 19122 Z= 0.284 Chirality : 0.039 0.147 2258 Planarity : 0.005 0.060 2459 Dihedral : 4.667 74.553 2028 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.03 % Allowed : 14.91 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.20), residues: 1863 helix: 1.91 (0.13), residues: 1432 sheet: -1.88 (0.71), residues: 48 loop : 0.27 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 79 TYR 0.013 0.001 TYR M 7 PHE 0.016 0.001 PHE M 172 TRP 0.011 0.001 TRP M 295 HIS 0.005 0.001 HIS N 557 Details of bonding type rmsd covalent geometry : bond 0.00344 (14133) covalent geometry : angle 0.56272 (19120) SS BOND : bond 0.00329 ( 1) SS BOND : angle 1.77272 ( 2) hydrogen bonds : bond 0.05831 ( 1114) hydrogen bonds : angle 3.68094 ( 3279) *********************** 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 199 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: N 50 ARG cc_start: 0.6456 (mtt90) cc_final: 0.5752 (mtp180) REVERT: N 54 ARG cc_start: 0.6788 (mpt90) cc_final: 0.6146 (mtm110) REVERT: N 66 THR cc_start: 0.8405 (t) cc_final: 0.8087 (m) REVERT: N 116 GLN cc_start: 0.6825 (pt0) cc_final: 0.6563 (mt0) REVERT: N 155 GLU cc_start: 0.6779 (tt0) cc_final: 0.5934 (tm-30) REVERT: N 215 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6455 (tm-30) REVERT: N 233 GLU cc_start: 0.7119 (tp30) cc_final: 0.6290 (mt-10) REVERT: N 306 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6594 (mm-30) REVERT: N 311 HIS cc_start: 0.5299 (m90) cc_final: 0.4387 (t70) REVERT: N 344 THR cc_start: 0.7575 (m) cc_final: 0.7374 (p) REVERT: N 397 LYS cc_start: 0.7381 (tttt) cc_final: 0.7149 (tmtt) REVERT: N 401 GLN cc_start: 0.7333 (tt0) cc_final: 0.6339 (mp10) REVERT: N 446 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7690 (mt) REVERT: N 453 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7734 (ttp-170) REVERT: N 525 GLN cc_start: 0.7111 (tp40) cc_final: 0.6778 (tp40) REVERT: N 543 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6587 (mtp85) REVERT: N 598 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6873 (mt) REVERT: N 606 LEU cc_start: 0.6863 (tt) cc_final: 0.6500 (mt) REVERT: O 47 GLU cc_start: 0.7008 (tp30) cc_final: 0.6267 (tt0) REVERT: P 11 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.5637 (m-30) REVERT: P 12 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6635 (mtm110) REVERT: S 47 GLU cc_start: 0.6243 (mt-10) cc_final: 0.5821 (tt0) REVERT: V 49 ARG cc_start: 0.7818 (mpt180) cc_final: 0.7403 (mmm160) REVERT: Z 47 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: M 59 ARG cc_start: 0.7292 (ttp-170) cc_final: 0.6633 (ttp-110) REVERT: M 65 GLN cc_start: 0.8341 (mt0) cc_final: 0.8045 (mm-40) REVERT: M 67 LYS cc_start: 0.7959 (mtpm) cc_final: 0.7313 (ptpt) REVERT: M 71 ASP cc_start: 0.8077 (p0) cc_final: 0.7578 (p0) REVERT: M 111 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7535 (tt0) REVERT: M 220 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7563 (mttt) REVERT: M 305 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.5393 (mtm-85) outliers start: 54 outliers final: 21 residues processed: 180 average time/residue: 0.7470 time to fit residues: 144.9438 Evaluate side-chains 159 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 180 VAL 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 595 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 P residue 11 ASP Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR 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 159 GLN Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 305 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 13 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 167 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 236 GLN M 26 GLN M 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124495 restraints weight = 15361.921| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.53 r_work: 0.3452 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14134 Z= 0.125 Angle : 0.499 6.329 19122 Z= 0.255 Chirality : 0.037 0.148 2258 Planarity : 0.005 0.059 2459 Dihedral : 4.522 77.089 2028 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.21 % Allowed : 15.88 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.20), residues: 1863 helix: 2.15 (0.13), residues: 1438 sheet: -1.80 (0.69), residues: 47 loop : 0.25 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 79 TYR 0.014 0.001 TYR M 7 PHE 0.015 0.001 PHE M 172 TRP 0.010 0.001 TRP M 295 HIS 0.003 0.001 HIS N 557 Details of bonding type rmsd covalent geometry : bond 0.00266 (14133) covalent geometry : angle 0.49852 (19120) SS BOND : bond 0.00718 ( 1) SS BOND : angle 1.85494 ( 2) hydrogen bonds : bond 0.05058 ( 1114) hydrogen bonds : angle 3.51753 ( 3279) *********************** 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 193 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 ARG cc_start: 0.6970 (mtt90) cc_final: 0.6377 (mtp180) REVERT: N 54 ARG cc_start: 0.7268 (mpt90) cc_final: 0.6926 (mtm110) REVERT: N 66 THR cc_start: 0.8703 (t) cc_final: 0.8412 (m) REVERT: N 116 GLN cc_start: 0.7431 (pt0) cc_final: 0.7212 (mt0) REVERT: N 155 GLU cc_start: 0.7147 (tt0) cc_final: 0.6478 (tm-30) REVERT: N 159 LYS cc_start: 0.7182 (mtmt) cc_final: 0.6878 (tptt) REVERT: N 233 GLU cc_start: 0.7539 (tp30) cc_final: 0.6948 (mt-10) REVERT: N 306 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7127 (mm-30) REVERT: N 311 HIS cc_start: 0.5515 (m90) cc_final: 0.4781 (t70) REVERT: N 401 GLN cc_start: 0.7475 (tt0) cc_final: 0.6781 (mp10) REVERT: N 446 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8140 (mt) REVERT: N 453 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8240 (ttp-170) REVERT: N 525 GLN cc_start: 0.7666 (tp40) cc_final: 0.7409 (tp40) REVERT: N 543 ARG cc_start: 0.7456 (mtp85) cc_final: 0.7231 (mtp85) REVERT: N 598 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7430 (mt) REVERT: N 606 LEU cc_start: 0.7693 (tt) cc_final: 0.7308 (mt) REVERT: O 47 GLU cc_start: 0.7479 (tp30) cc_final: 0.7016 (tt0) REVERT: P 11 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.6388 (m-30) REVERT: P 12 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7424 (mtm110) REVERT: S 47 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6462 (tt0) REVERT: V 49 ARG cc_start: 0.7969 (mpt180) cc_final: 0.7744 (mmm160) REVERT: Z 47 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: M 59 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7495 (ttp-110) REVERT: M 67 LYS cc_start: 0.8357 (mtpm) cc_final: 0.7826 (ptpt) REVERT: M 71 ASP cc_start: 0.8099 (p0) cc_final: 0.7629 (p0) REVERT: M 111 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7910 (tt0) outliers start: 43 outliers final: 17 residues processed: 177 average time/residue: 0.7642 time to fit residues: 145.9321 Evaluate side-chains 156 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 138 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 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 595 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain U residue 47 GLU 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 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 177 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** O 51 ASN Z 51 ASN M 26 GLN M 65 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 = 0.3704 r_free = 0.3704 target = 0.145962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102892 restraints weight = 14880.895| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.69 r_work: 0.3178 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14134 Z= 0.155 Angle : 0.550 7.488 19122 Z= 0.279 Chirality : 0.039 0.156 2258 Planarity : 0.005 0.061 2459 Dihedral : 4.602 78.897 2028 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.36 % Allowed : 15.96 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.19), residues: 1863 helix: 2.04 (0.13), residues: 1439 sheet: -1.74 (0.68), residues: 48 loop : 0.17 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 79 TYR 0.016 0.001 TYR M 7 PHE 0.016 0.001 PHE M 172 TRP 0.010 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00359 (14133) covalent geometry : angle 0.54873 (19120) SS BOND : bond 0.01763 ( 1) SS BOND : angle 3.88330 ( 2) hydrogen bonds : bond 0.05898 ( 1114) hydrogen bonds : angle 3.63249 ( 3279) *********************** 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 185 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: N 50 ARG cc_start: 0.6585 (mtt90) cc_final: 0.5983 (mtp85) REVERT: N 54 ARG cc_start: 0.6833 (mpt90) cc_final: 0.6154 (mtm110) REVERT: N 66 THR cc_start: 0.8460 (t) cc_final: 0.8129 (m) REVERT: N 155 GLU cc_start: 0.6650 (tt0) cc_final: 0.5963 (tm-30) REVERT: N 159 LYS cc_start: 0.6782 (mtmt) cc_final: 0.6548 (tmtm) REVERT: N 218 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7111 (mtm110) REVERT: N 306 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6507 (mm-30) REVERT: N 311 HIS cc_start: 0.5518 (m90) cc_final: 0.4426 (t70) REVERT: N 401 GLN cc_start: 0.7484 (tt0) cc_final: 0.6469 (mp10) REVERT: N 446 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7778 (mt) REVERT: N 453 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7779 (ttp-170) REVERT: N 490 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6397 (mpp-170) REVERT: N 492 MET cc_start: 0.7904 (mmt) cc_final: 0.7467 (mmt) REVERT: N 525 GLN cc_start: 0.7034 (tp40) cc_final: 0.6768 (tp40) REVERT: N 543 ARG cc_start: 0.7037 (mtp85) cc_final: 0.6788 (mtp85) REVERT: N 598 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6854 (mt) REVERT: N 606 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6658 (mt) REVERT: O 47 GLU cc_start: 0.7239 (tp30) cc_final: 0.6498 (tt0) REVERT: O 79 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7292 (mmt90) REVERT: P 11 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.5626 (m-30) REVERT: P 12 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6585 (mtm110) REVERT: S 47 GLU cc_start: 0.6235 (mt-10) cc_final: 0.5762 (tt0) REVERT: V 49 ARG cc_start: 0.7838 (mpt180) cc_final: 0.7460 (mmm160) REVERT: W 63 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7851 (mm-30) REVERT: W 79 ARG cc_start: 0.7041 (mtp85) cc_final: 0.6768 (mtp85) REVERT: Z 47 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: M 27 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: M 59 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6683 (ttp80) REVERT: M 71 ASP cc_start: 0.8101 (p0) cc_final: 0.7605 (p0) REVERT: M 111 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7601 (tt0) REVERT: M 305 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.5519 (mtm-85) outliers start: 45 outliers final: 20 residues processed: 168 average time/residue: 0.8276 time to fit residues: 149.0055 Evaluate side-chains 160 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 LEU 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 310 GLU 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 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 P residue 11 ASP Chi-restraints excluded: chain R residue 50 SER 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 Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 27 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 205 PHE Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain M residue 305 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 116 GLN 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 = 0.3716 r_free = 0.3716 target = 0.147145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104163 restraints weight = 14809.118| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.68 r_work: 0.3199 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14134 Z= 0.140 Angle : 0.528 7.131 19122 Z= 0.268 Chirality : 0.038 0.154 2258 Planarity : 0.005 0.057 2459 Dihedral : 4.568 79.861 2028 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.83 % Allowed : 16.85 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.19), residues: 1863 helix: 2.16 (0.13), residues: 1433 sheet: -1.43 (0.70), residues: 48 loop : 0.06 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 79 TYR 0.016 0.001 TYR M 7 PHE 0.015 0.001 PHE M 172 TRP 0.010 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00316 (14133) covalent geometry : angle 0.52610 (19120) SS BOND : bond 0.00517 ( 1) SS BOND : angle 4.22869 ( 2) hydrogen bonds : bond 0.05409 ( 1114) hydrogen bonds : angle 3.55789 ( 3279) *********************** 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 179 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6799 (mpt90) cc_final: 0.6135 (mtm110) REVERT: N 66 THR cc_start: 0.8466 (t) cc_final: 0.8172 (m) REVERT: N 155 GLU cc_start: 0.6663 (tt0) cc_final: 0.5976 (tm-30) REVERT: N 215 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6854 (tm-30) REVERT: N 218 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7062 (mtm110) REVERT: N 237 HIS cc_start: 0.7113 (OUTLIER) cc_final: 0.6837 (m-70) REVERT: N 306 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6502 (mm-30) REVERT: N 311 HIS cc_start: 0.5384 (m90) cc_final: 0.4376 (t70) REVERT: N 401 GLN cc_start: 0.7285 (tt0) cc_final: 0.6302 (mp10) REVERT: N 446 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7769 (mt) REVERT: N 453 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7619 (ttp-170) REVERT: N 525 GLN cc_start: 0.7002 (tp40) cc_final: 0.6660 (tp40) REVERT: N 543 ARG cc_start: 0.7038 (mtp85) cc_final: 0.6837 (mtp85) REVERT: N 598 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6713 (mt) REVERT: N 606 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6670 (mt) REVERT: O 47 GLU cc_start: 0.7214 (tp30) cc_final: 0.6495 (tt0) REVERT: O 79 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7172 (mmt90) REVERT: P 11 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.5546 (m-30) REVERT: P 12 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6531 (mtm110) REVERT: R 49 ARG cc_start: 0.7495 (mpt180) cc_final: 0.7060 (mmm160) REVERT: U 49 ARG cc_start: 0.7716 (mpt90) cc_final: 0.6961 (mmm160) REVERT: V 49 ARG cc_start: 0.7875 (mpt180) cc_final: 0.7494 (mmm160) REVERT: Z 47 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: M 59 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6515 (ttp80) REVERT: M 67 LYS cc_start: 0.7904 (mtpm) cc_final: 0.7304 (ptpt) REVERT: M 71 ASP cc_start: 0.8080 (p0) cc_final: 0.7606 (p0) REVERT: M 111 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7574 (tt0) REVERT: M 305 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.5482 (mtm-85) outliers start: 38 outliers final: 17 residues processed: 163 average time/residue: 0.8417 time to fit residues: 147.4968 Evaluate side-chains 160 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 386 ASN Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 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 P residue 11 ASP 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 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain M residue 305 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 178 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 1 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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** 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 = 0.3793 r_free = 0.3793 target = 0.151741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112069 restraints weight = 15099.683| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.53 r_work: 0.3293 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.7635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14134 Z= 0.149 Angle : 0.542 8.209 19122 Z= 0.275 Chirality : 0.038 0.160 2258 Planarity : 0.005 0.058 2459 Dihedral : 4.577 80.405 2028 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.98 % Allowed : 17.08 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.19), residues: 1863 helix: 2.10 (0.13), residues: 1435 sheet: -1.35 (0.71), residues: 48 loop : -0.09 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 79 TYR 0.016 0.001 TYR M 7 PHE 0.015 0.001 PHE M 172 TRP 0.010 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00343 (14133) covalent geometry : angle 0.54114 (19120) SS BOND : bond 0.00278 ( 1) SS BOND : angle 3.67611 ( 2) hydrogen bonds : bond 0.05714 ( 1114) hydrogen bonds : angle 3.60820 ( 3279) *********************** 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 181 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.7171 (mpt90) cc_final: 0.6613 (mtm110) REVERT: N 66 THR cc_start: 0.8681 (t) cc_final: 0.8343 (m) REVERT: N 155 GLU cc_start: 0.7001 (tt0) cc_final: 0.6222 (tm-30) REVERT: N 215 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7070 (tm-30) REVERT: N 218 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7392 (mtm110) REVERT: N 237 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.7147 (m-70) REVERT: N 306 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6626 (tt0) REVERT: N 311 HIS cc_start: 0.5627 (m90) cc_final: 0.4699 (t70) REVERT: N 384 LYS cc_start: 0.7491 (tmmt) cc_final: 0.7261 (tttp) REVERT: N 401 GLN cc_start: 0.7563 (tt0) cc_final: 0.6691 (mp10) REVERT: N 446 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7989 (OUTLIER) REVERT: N 453 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7913 (ttp-170) REVERT: N 492 MET cc_start: 0.8244 (mmt) cc_final: 0.7966 (mmt) REVERT: N 525 GLN cc_start: 0.7389 (tp40) cc_final: 0.7109 (tp40) REVERT: N 598 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7183 (mt) REVERT: N 606 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7060 (mt) REVERT: O 47 GLU cc_start: 0.7502 (tp30) cc_final: 0.6869 (tt0) REVERT: O 79 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7544 (mmt90) REVERT: P 11 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.5877 (m-30) REVERT: P 12 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6982 (mtm110) REVERT: P 49 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7193 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7694 (ttm-80) REVERT: R 49 ARG cc_start: 0.7620 (mpt180) cc_final: 0.7332 (mmm160) REVERT: S 47 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6226 (tt0) REVERT: T 79 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6905 (mtt180) REVERT: U 49 ARG cc_start: 0.7888 (mpt90) cc_final: 0.7251 (mmm160) REVERT: V 49 ARG cc_start: 0.7958 (mpt180) cc_final: 0.7615 (mmm160) REVERT: Z 47 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: M 30 ASP cc_start: 0.7714 (p0) cc_final: 0.7417 (m-30) REVERT: M 59 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7053 (ttp80) REVERT: M 67 LYS cc_start: 0.8221 (mtpm) cc_final: 0.7597 (ptpt) REVERT: M 71 ASP cc_start: 0.8181 (p0) cc_final: 0.7702 (p0) REVERT: M 111 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7785 (tt0) REVERT: M 305 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.5956 (mtm-85) outliers start: 40 outliers final: 18 residues processed: 165 average time/residue: 0.8842 time to fit residues: 156.0978 Evaluate side-chains 162 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL 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 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 P residue 11 ASP 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 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 305 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 297 HIS N 616 HIS 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 = 0.3721 r_free = 0.3721 target = 0.147740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105584 restraints weight = 14399.088| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.54 r_work: 0.3101 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14134 Z= 0.153 Angle : 0.549 8.258 19122 Z= 0.278 Chirality : 0.039 0.159 2258 Planarity : 0.005 0.058 2459 Dihedral : 4.592 80.969 2028 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.68 % Allowed : 17.67 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.19), residues: 1863 helix: 2.07 (0.13), residues: 1435 sheet: -1.38 (0.71), residues: 48 loop : -0.20 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 79 TYR 0.017 0.001 TYR M 7 PHE 0.015 0.001 PHE M 172 TRP 0.010 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00356 (14133) covalent geometry : angle 0.54849 (19120) SS BOND : bond 0.00940 ( 1) SS BOND : angle 2.30507 ( 2) hydrogen bonds : bond 0.05770 ( 1114) hydrogen bonds : angle 3.61468 ( 3279) *********************** 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 180 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.7328 (mpt90) cc_final: 0.6726 (mtm110) REVERT: N 66 THR cc_start: 0.8790 (t) cc_final: 0.8464 (m) REVERT: N 155 GLU cc_start: 0.7103 (tt0) cc_final: 0.6342 (tm-30) REVERT: N 215 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7160 (tm-30) REVERT: N 218 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7517 (mtm110) REVERT: N 237 HIS cc_start: 0.7497 (OUTLIER) cc_final: 0.7295 (m-70) REVERT: N 306 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6838 (tt0) REVERT: N 311 HIS cc_start: 0.5770 (m90) cc_final: 0.4811 (t70) REVERT: N 384 LYS cc_start: 0.7590 (tmmt) cc_final: 0.7356 (tttp) REVERT: N 401 GLN cc_start: 0.7691 (tt0) cc_final: 0.6825 (mp10) REVERT: N 453 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8050 (ttp-170) REVERT: N 525 GLN cc_start: 0.7449 (tp40) cc_final: 0.7181 (tp40) REVERT: N 598 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7171 (mt) REVERT: N 606 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7234 (mt) REVERT: O 47 GLU cc_start: 0.7742 (tp30) cc_final: 0.7124 (tt0) REVERT: O 79 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7796 (mmt90) REVERT: P 11 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.6104 (m-30) REVERT: P 12 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7248 (mtm110) REVERT: P 49 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7267 (mmt-90) REVERT: Q 49 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7781 (mtp85) REVERT: R 49 ARG cc_start: 0.7608 (mpt180) cc_final: 0.7398 (mmm160) REVERT: U 49 ARG cc_start: 0.8080 (mpt90) cc_final: 0.7481 (mmm160) REVERT: V 49 ARG cc_start: 0.8129 (mpt180) cc_final: 0.7803 (mmm160) REVERT: Z 47 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: M 30 ASP cc_start: 0.7764 (p0) cc_final: 0.7415 (m-30) REVERT: M 52 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: M 59 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.7391 (ttp80) REVERT: M 67 LYS cc_start: 0.8332 (mtpm) cc_final: 0.7726 (ptpt) REVERT: M 71 ASP cc_start: 0.8267 (p0) cc_final: 0.7805 (p0) REVERT: M 111 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7948 (tt0) REVERT: M 305 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6352 (mtm-85) outliers start: 36 outliers final: 17 residues processed: 166 average time/residue: 0.8524 time to fit residues: 151.8846 Evaluate side-chains 165 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL 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 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU 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 P residue 11 ASP 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 52 GLN Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain M residue 305 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 183 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106466 restraints weight = 14257.964| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.66 r_work: 0.3120 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.7784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14134 Z= 0.131 Angle : 0.514 8.250 19122 Z= 0.262 Chirality : 0.037 0.156 2258 Planarity : 0.005 0.055 2459 Dihedral : 4.496 80.814 2028 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.24 % Allowed : 18.12 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.19), residues: 1863 helix: 2.23 (0.13), residues: 1437 sheet: -1.26 (0.74), residues: 48 loop : -0.18 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 12 TYR 0.015 0.001 TYR M 7 PHE 0.014 0.001 PHE M 172 TRP 0.011 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00288 (14133) covalent geometry : angle 0.51366 (19120) SS BOND : bond 0.00673 ( 1) SS BOND : angle 2.81367 ( 2) hydrogen bonds : bond 0.05184 ( 1114) hydrogen bonds : angle 3.53076 ( 3279) ********************** 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 173 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: N 54 ARG cc_start: 0.7248 (mpt90) cc_final: 0.6645 (mtm110) REVERT: N 66 THR cc_start: 0.8771 (t) cc_final: 0.8446 (m) REVERT: N 155 GLU cc_start: 0.7048 (tt0) cc_final: 0.6303 (tm-30) REVERT: N 215 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7057 (tm-30) REVERT: N 218 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7393 (mtm110) REVERT: N 237 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.7261 (m-70) REVERT: N 306 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6824 (tt0) REVERT: N 311 HIS cc_start: 0.5649 (m90) cc_final: 0.4714 (t70) REVERT: N 384 LYS cc_start: 0.7522 (tmmt) cc_final: 0.7300 (tttp) REVERT: N 401 GLN cc_start: 0.7544 (tt0) cc_final: 0.6660 (mp10) REVERT: N 453 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7991 (ttp-170) REVERT: N 525 GLN cc_start: 0.7380 (tp40) cc_final: 0.7104 (tp40) REVERT: N 598 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7068 (mt) REVERT: N 606 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7154 (mt) REVERT: O 47 GLU cc_start: 0.7641 (tp30) cc_final: 0.7014 (tt0) REVERT: O 79 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7756 (mmt90) REVERT: P 11 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.6158 (m-30) REVERT: P 12 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7144 (mtm110) REVERT: P 49 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7197 (mmt-90) REVERT: Q 49 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7708 (mtp85) REVERT: R 49 ARG cc_start: 0.7575 (mpt180) cc_final: 0.7345 (mmm160) REVERT: V 49 ARG cc_start: 0.8144 (mpt180) cc_final: 0.7930 (tpt-90) REVERT: Z 47 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: M 30 ASP cc_start: 0.7731 (p0) cc_final: 0.7379 (m-30) REVERT: M 59 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7230 (ttp80) REVERT: M 67 LYS cc_start: 0.8273 (mtpm) cc_final: 0.7717 (ptpt) REVERT: M 71 ASP cc_start: 0.8259 (p0) cc_final: 0.7786 (p0) REVERT: M 111 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7938 (tt0) REVERT: M 305 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.6255 (mtm-85) outliers start: 30 outliers final: 14 residues processed: 162 average time/residue: 0.8481 time to fit residues: 147.2257 Evaluate side-chains 161 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL 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 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 516 LEU 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 P residue 11 ASP 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 59 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain M residue 305 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 123 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** 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 = 0.3762 r_free = 0.3762 target = 0.151392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.106510 restraints weight = 14221.370| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.65 r_work: 0.3121 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14134 Z= 0.132 Angle : 0.511 6.959 19122 Z= 0.261 Chirality : 0.037 0.157 2258 Planarity : 0.005 0.054 2459 Dihedral : 4.457 80.737 2028 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.01 % Allowed : 18.49 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.19), residues: 1863 helix: 2.24 (0.13), residues: 1438 sheet: -1.26 (0.73), residues: 48 loop : -0.23 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 12 TYR 0.016 0.001 TYR M 7 PHE 0.014 0.001 PHE M 172 TRP 0.011 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 Details of bonding type rmsd covalent geometry : bond 0.00290 (14133) covalent geometry : angle 0.51092 (19120) SS BOND : bond 0.00632 ( 1) SS BOND : angle 2.29608 ( 2) hydrogen bonds : bond 0.05193 ( 1114) hydrogen bonds : angle 3.52338 ( 3279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5368.54 seconds wall clock time: 91 minutes 51.39 seconds (5511.39 seconds total)