Starting phenix.real_space_refine on Mon Dec 30 19:36:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywt_39644/12_2024/8ywt_39644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywt_39644/12_2024/8ywt_39644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywt_39644/12_2024/8ywt_39644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywt_39644/12_2024/8ywt_39644.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywt_39644/12_2024/8ywt_39644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywt_39644/12_2024/8ywt_39644.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 9026 2.51 5 N 2432 2.21 5 O 2504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13986 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 5089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5089 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 613} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 524 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "R" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "S" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "T" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "U" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "V" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 504 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "W" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "X" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Y" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Z" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "M" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 308} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 88 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 80 Classifications: {'peptide': 20} Incomplete info: {'backbone_only': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 8.74, per 1000 atoms: 0.62 Number of scatterers: 13986 At special positions: 0 Unit cell: (99.44, 124.96, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 2504 8.00 N 2432 7.00 C 9026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 6 sheets defined 81.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'N' and resid 20 through 31 Processing helix chain 'N' and resid 46 through 70 Processing helix chain 'N' and resid 83 through 129 Proline residue: N 93 - end of helix removed outlier: 4.592A pdb=" N GLU N 120 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Proline residue: N 121 - end of helix Processing helix chain 'N' and resid 131 through 135 Processing helix chain 'N' and resid 149 through 161 removed outlier: 3.668A pdb=" N VAL N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 197 Processing helix chain 'N' and resid 206 through 211 Processing helix chain 'N' and resid 212 through 266 removed outlier: 4.174A pdb=" N ARG N 218 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG N 219 " --> pdb=" O GLU N 215 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU N 220 " --> pdb=" O ALA N 216 " (cutoff:3.500A) Proline residue: N 228 - end of helix removed outlier: 5.723A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'N' and resid 286 through 296 removed outlier: 3.637A pdb=" N VAL N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG N 296 " --> pdb=" O GLU N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 334 Processing helix chain 'N' and resid 347 through 349 No H-bonds generated for 'chain 'N' and resid 347 through 349' Processing helix chain 'N' and resid 350 through 364 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 386 removed outlier: 3.526A pdb=" N GLY N 381 " --> pdb=" O ARG N 377 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR N 382 " --> pdb=" O TRP N 378 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 395 Processing helix chain 'N' and resid 399 through 424 removed outlier: 3.783A pdb=" N LYS N 405 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 435 Processing helix chain 'N' and resid 455 through 488 removed outlier: 6.317A pdb=" N ASN N 461 " --> pdb=" O ALA N 457 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU N 462 " --> pdb=" O LYS N 458 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE N 470 " --> pdb=" O LEU N 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 516 removed outlier: 3.555A pdb=" N GLU N 497 " --> pdb=" O ALA N 493 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 543 removed outlier: 3.987A pdb=" N TYR N 529 " --> pdb=" O GLN N 525 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 560 removed outlier: 4.990A pdb=" N PHE N 552 " --> pdb=" O ILE N 548 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 589 removed outlier: 3.570A pdb=" N GLY N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU N 589 " --> pdb=" O LEU N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 626 removed outlier: 4.934A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 4.072A pdb=" N LEU N 623 " --> pdb=" O GLN N 619 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU N 624 " --> pdb=" O PRO N 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 48 removed outlier: 4.079A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU O 47 " --> pdb=" O GLY O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 63 through 78 removed outlier: 3.759A pdb=" N GLY O 78 " --> pdb=" O PHE O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 48 removed outlier: 3.537A pdb=" N LEU P 10 " --> pdb=" O ALA P 6 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG P 12 " --> pdb=" O GLY P 8 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 16 " --> pdb=" O ARG P 12 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 78 Processing helix chain 'Q' and resid 8 through 48 removed outlier: 3.516A pdb=" N VAL Q 17 " --> pdb=" O GLY Q 13 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA Q 26 " --> pdb=" O ALA Q 22 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 Processing helix chain 'Q' and resid 64 through 78 Processing helix chain 'R' and resid 10 through 48 removed outlier: 3.620A pdb=" N ALA R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 Processing helix chain 'R' and resid 65 through 78 removed outlier: 3.576A pdb=" N GLY R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 48 removed outlier: 3.890A pdb=" N ALA S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA S 26 " --> pdb=" O ALA S 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA S 33 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN S 34 " --> pdb=" O THR S 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA S 35 " --> pdb=" O GLY S 31 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 65 through 78 Processing helix chain 'T' and resid 9 through 48 removed outlier: 3.598A pdb=" N LEU T 14 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA T 46 " --> pdb=" O VAL T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 Processing helix chain 'T' and resid 62 through 64 No H-bonds generated for 'chain 'T' and resid 62 through 64' Processing helix chain 'T' and resid 65 through 78 removed outlier: 3.558A pdb=" N GLY T 69 " --> pdb=" O LEU T 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 48 removed outlier: 4.433A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU U 47 " --> pdb=" O GLY U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'U' and resid 65 through 78 removed outlier: 3.512A pdb=" N GLY U 69 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE U 72 " --> pdb=" O PHE U 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 48 removed outlier: 3.585A pdb=" N ALA V 26 " --> pdb=" O ALA V 22 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 63 through 78 removed outlier: 3.537A pdb=" N PHE V 68 " --> pdb=" O THR V 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 46 removed outlier: 3.588A pdb=" N ALA W 16 " --> pdb=" O ARG W 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 50 No H-bonds generated for 'chain 'W' and resid 48 through 50' Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 63 through 78 Processing helix chain 'X' and resid 9 through 48 removed outlier: 3.598A pdb=" N LEU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL X 17 " --> pdb=" O GLY X 13 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY X 43 " --> pdb=" O ALA X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.996A pdb=" N PHE X 58 " --> pdb=" O THR X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 80 removed outlier: 3.769A pdb=" N GLY X 78 " --> pdb=" O PHE X 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG X 79 " --> pdb=" O ILE X 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 48 removed outlier: 4.368A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 62 through 64 No H-bonds generated for 'chain 'Y' and resid 62 through 64' Processing helix chain 'Y' and resid 65 through 78 removed outlier: 3.601A pdb=" N ILE Y 72 " --> pdb=" O PHE Y 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 48 removed outlier: 3.569A pdb=" N ALA Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY Z 43 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 Processing helix chain 'Z' and resid 64 through 80 removed outlier: 3.568A pdb=" N ARG Z 79 " --> pdb=" O ILE Z 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 17 removed outlier: 3.647A pdb=" N ALA M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 28 removed outlier: 4.170A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 32 through 42 removed outlier: 3.537A pdb=" N GLU M 42 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 48 removed outlier: 3.648A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 69 removed outlier: 3.515A pdb=" N LYS M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.879A pdb=" N VAL M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 106 removed outlier: 3.859A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU M 87 " --> pdb=" O ALA M 83 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU M 88 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 112 removed outlier: 3.650A pdb=" N VAL M 112 " --> pdb=" O PHE M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 129 Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 145 through 158 removed outlier: 4.180A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA M 153 " --> pdb=" O ARG M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 181 Processing helix chain 'M' and resid 185 through 207 removed outlier: 3.632A pdb=" N ARG M 189 " --> pdb=" O GLN M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 218 Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 238 through 243 Processing helix chain 'M' and resid 257 through 275 removed outlier: 3.798A pdb=" N CYS M 267 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS M 275 " --> pdb=" O LYS M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 279 Processing helix chain 'M' and resid 282 through 310 removed outlier: 4.373A pdb=" N VAL M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG M 305 " --> pdb=" O ARG M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 317 removed outlier: 4.648A pdb=" N VAL M 316 " --> pdb=" O PRO M 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 Processing helix chain 'K' and resid 32 through 41 Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 10 through 17 Processing helix chain 'L' and resid 18 through 21 removed outlier: 3.590A pdb=" N GLN L 21 " --> pdb=" O ALA L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 18 through 21' Processing sheet with id=AA1, first strand: chain 'N' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'N' and resid 14 through 15 Processing sheet with id=AA3, first strand: chain 'N' and resid 138 through 145 Processing sheet with id=AA4, first strand: chain 'N' and resid 318 through 319 Processing sheet with id=AA5, first strand: chain 'N' and resid 389 through 391 Processing sheet with id=AA6, first strand: chain 'N' and resid 438 through 439 1114 hydrogen bonds defined for protein. 3279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 3.84 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.390 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.103 14133 Z= 0.826 Angle : 1.926 12.824 19120 Z= 1.327 Chirality : 0.091 0.432 2258 Planarity : 0.019 0.303 2459 Dihedral : 14.343 86.972 5007 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.09 % Favored : 97.64 % Rotamer: Outliers : 3.36 % Allowed : 6.64 % Favored : 90.01 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 1863 helix: -0.89 (0.12), residues: 1411 sheet: -1.18 (0.71), residues: 55 loop : -0.38 (0.34), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.019 TRP N 545 HIS 0.013 0.004 HIS N 297 PHE 0.070 0.013 PHE X 68 TYR 0.150 0.024 TYR N 118 ARG 0.013 0.001 ARG M 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.432 Fit side-chains REVERT: N 155 GLU cc_start: 0.6652 (tt0) cc_final: 0.5848 (tm-30) REVERT: N 306 GLU cc_start: 0.6246 (mt-10) cc_final: 0.6041 (mm-30) REVERT: N 322 ASP cc_start: 0.6111 (t0) cc_final: 0.5886 (t0) REVERT: N 401 GLN cc_start: 0.6985 (tt0) cc_final: 0.6279 (mp10) REVERT: N 544 ILE cc_start: 0.6305 (mt) cc_final: 0.6057 (mt) REVERT: N 606 LEU cc_start: 0.6563 (tt) cc_final: 0.6362 (tp) REVERT: N 622 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7455 (ptm160) REVERT: U 30 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7945 (m) REVERT: Y 11 ASP cc_start: 0.6852 (t0) cc_final: 0.6310 (t70) REVERT: M 21 LYS cc_start: 0.6540 (mtpt) cc_final: 0.6288 (pttm) REVERT: M 232 ARG cc_start: 0.6809 (mtm110) cc_final: 0.6219 (ttp-170) REVERT: M 291 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5598 (mmtt) outliers start: 45 outliers final: 8 residues processed: 252 average time/residue: 1.2162 time to fit residues: 339.1367 Evaluate side-chains 127 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 567 VAL Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain R residue 62 PRO Chi-restraints excluded: chain S residue 62 PRO Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 291 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 25 GLN N 106 GLN N 250 GLN N 408 HIS N 525 GLN R 51 ASN T 51 ASN U 51 ASN W 51 ASN X 34 GLN X 51 ASN M 91 ASN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14133 Z= 0.247 Angle : 0.691 9.866 19120 Z= 0.350 Chirality : 0.043 0.178 2258 Planarity : 0.006 0.047 2459 Dihedral : 5.389 56.149 2050 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.88 % Allowed : 11.33 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1863 helix: 0.96 (0.13), residues: 1435 sheet: -1.74 (0.71), residues: 47 loop : 0.68 (0.38), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 625 HIS 0.007 0.002 HIS N 491 PHE 0.016 0.002 PHE N 470 TYR 0.009 0.001 TYR N 165 ARG 0.009 0.001 ARG M 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: N 155 GLU cc_start: 0.6612 (tt0) cc_final: 0.5810 (tm-30) REVERT: N 233 GLU cc_start: 0.6756 (tp30) cc_final: 0.5919 (tt0) REVERT: N 306 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6201 (mm-30) REVERT: N 401 GLN cc_start: 0.6696 (tt0) cc_final: 0.6297 (mp10) REVERT: N 413 MET cc_start: 0.7505 (mtp) cc_final: 0.7225 (mtp) REVERT: N 453 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6827 (ttp-170) REVERT: N 484 TYR cc_start: 0.6916 (t80) cc_final: 0.6686 (t80) REVERT: N 598 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6164 (mt) REVERT: N 606 LEU cc_start: 0.6695 (tt) cc_final: 0.6465 (mp) REVERT: N 627 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: N 638 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7542 (m-40) REVERT: Q 12 ARG cc_start: 0.6085 (mtp180) cc_final: 0.5702 (mtp85) REVERT: U 79 ARG cc_start: 0.6671 (mmt180) cc_final: 0.6469 (mmt180) REVERT: X 12 ARG cc_start: 0.6629 (tpt170) cc_final: 0.6291 (mtp85) REVERT: M 21 LYS cc_start: 0.7628 (mtpt) cc_final: 0.7396 (mttt) REVERT: M 120 ARG cc_start: 0.7031 (mtt-85) cc_final: 0.6682 (mtt-85) REVERT: M 149 ARG cc_start: 0.6048 (ttm170) cc_final: 0.5765 (ttp80) REVERT: M 181 LYS cc_start: 0.6858 (ptpt) cc_final: 0.6653 (ptpt) REVERT: M 190 ASP cc_start: 0.6581 (t0) cc_final: 0.6008 (m-30) REVERT: M 205 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.5066 (t80) REVERT: M 291 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7435 (mmpt) outliers start: 52 outliers final: 7 residues processed: 218 average time/residue: 1.5554 time to fit residues: 366.2161 Evaluate side-chains 133 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 308 VAL Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 627 GLU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 205 PHE Chi-restraints excluded: chain M residue 291 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 180 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 25 GLN N 65 HIS N 250 GLN N 311 HIS N 323 ASN N 616 HIS V 51 ASN M 94 HIS M 145 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14133 Z= 0.348 Angle : 0.699 8.353 19120 Z= 0.349 Chirality : 0.043 0.161 2258 Planarity : 0.006 0.059 2459 Dihedral : 5.117 67.551 2032 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.77 % Allowed : 13.87 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 1863 helix: 1.31 (0.13), residues: 1432 sheet: -1.69 (0.76), residues: 43 loop : 0.34 (0.35), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 295 HIS 0.008 0.002 HIS N 557 PHE 0.020 0.002 PHE Z 68 TYR 0.017 0.002 TYR N 43 ARG 0.007 0.001 ARG M 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 1.827 Fit side-chains REVERT: N 6 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: N 22 GLN cc_start: 0.5728 (mt0) cc_final: 0.5506 (mt0) REVERT: N 50 ARG cc_start: 0.6134 (mtt90) cc_final: 0.5677 (mtp180) REVERT: N 54 ARG cc_start: 0.6179 (mpt90) cc_final: 0.5632 (mtm110) REVERT: N 155 GLU cc_start: 0.6578 (tt0) cc_final: 0.5862 (tm-30) REVERT: N 222 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6860 (pt0) REVERT: N 233 GLU cc_start: 0.6917 (tp30) cc_final: 0.6028 (mt-10) REVERT: N 306 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6250 (mm-30) REVERT: N 311 HIS cc_start: 0.5438 (m90) cc_final: 0.4648 (t70) REVERT: N 344 THR cc_start: 0.7234 (m) cc_final: 0.6890 (p) REVERT: N 401 GLN cc_start: 0.7237 (tt0) cc_final: 0.6491 (mp10) REVERT: N 413 MET cc_start: 0.7617 (mtp) cc_final: 0.7397 (mtp) REVERT: N 453 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7227 (ttp-170) REVERT: N 484 TYR cc_start: 0.7181 (t80) cc_final: 0.6861 (t80) REVERT: N 492 MET cc_start: 0.7094 (mmm) cc_final: 0.6870 (mmt) REVERT: N 515 TYR cc_start: 0.5211 (m-80) cc_final: 0.4922 (m-80) REVERT: N 525 GLN cc_start: 0.6898 (tp40) cc_final: 0.6607 (tp40) REVERT: N 598 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6399 (mt) REVERT: N 606 LEU cc_start: 0.6751 (tt) cc_final: 0.6404 (mt) REVERT: O 47 GLU cc_start: 0.7045 (tp30) cc_final: 0.6560 (tt0) REVERT: P 11 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.5070 (m-30) REVERT: Q 12 ARG cc_start: 0.5993 (mtp180) cc_final: 0.5615 (mtp85) REVERT: T 19 MET cc_start: 0.6579 (mtp) cc_final: 0.6373 (mtp) REVERT: U 79 ARG cc_start: 0.6739 (mmt180) cc_final: 0.6405 (mmt180) REVERT: W 79 ARG cc_start: 0.6548 (mtt-85) cc_final: 0.6317 (mtp85) REVERT: X 12 ARG cc_start: 0.6608 (tpt170) cc_final: 0.6256 (mtp85) REVERT: Z 12 ARG cc_start: 0.5662 (OUTLIER) cc_final: 0.5419 (ttp80) REVERT: Z 47 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: M 21 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7770 (mtmm) REVERT: M 29 LEU cc_start: 0.8050 (tp) cc_final: 0.7835 (tp) REVERT: M 59 ARG cc_start: 0.6793 (ttp-170) cc_final: 0.6381 (ttp-110) REVERT: M 67 LYS cc_start: 0.8098 (mtpm) cc_final: 0.7405 (mtmt) REVERT: M 71 ASP cc_start: 0.8193 (p0) cc_final: 0.7701 (p0) REVERT: M 126 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6894 (mm-40) REVERT: M 190 ASP cc_start: 0.6633 (t0) cc_final: 0.6430 (m-30) REVERT: M 291 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7699 (UNCLASSIFIED) REVERT: M 301 ARG cc_start: 0.7291 (mmm160) cc_final: 0.6760 (ttt90) outliers start: 64 outliers final: 20 residues processed: 215 average time/residue: 1.7147 time to fit residues: 396.5176 Evaluate side-chains 166 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 222 GLU Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 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 30 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 159 GLN Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain M residue 291 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 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 116 GLN N 236 GLN N 605 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14133 Z= 0.197 Angle : 0.538 7.580 19120 Z= 0.274 Chirality : 0.038 0.139 2258 Planarity : 0.005 0.062 2459 Dihedral : 4.809 73.487 2032 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.58 % Allowed : 15.59 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.20), residues: 1863 helix: 1.84 (0.13), residues: 1438 sheet: -1.88 (0.69), residues: 48 loop : 0.30 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 PHE 0.017 0.001 PHE M 172 TYR 0.014 0.001 TYR M 7 ARG 0.007 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 1.539 Fit side-chains REVERT: N 50 ARG cc_start: 0.6011 (mtt90) cc_final: 0.5449 (mtp180) REVERT: N 54 ARG cc_start: 0.6069 (mpt90) cc_final: 0.5610 (mtm110) REVERT: N 66 THR cc_start: 0.7901 (t) cc_final: 0.7644 (m) REVERT: N 155 GLU cc_start: 0.6459 (tt0) cc_final: 0.5718 (tm-30) REVERT: N 233 GLU cc_start: 0.6757 (tp30) cc_final: 0.6035 (mt-10) REVERT: N 306 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6330 (mm-30) REVERT: N 311 HIS cc_start: 0.5277 (m90) cc_final: 0.4401 (t70) REVERT: N 344 THR cc_start: 0.6965 (m) cc_final: 0.6620 (p) REVERT: N 401 GLN cc_start: 0.6928 (tt0) cc_final: 0.6204 (mp10) REVERT: N 446 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7145 (mt) REVERT: N 453 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7176 (ttp-170) REVERT: N 484 TYR cc_start: 0.7082 (t80) cc_final: 0.6790 (t80) REVERT: N 490 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6092 (mpp-170) REVERT: N 492 MET cc_start: 0.7083 (mmm) cc_final: 0.6797 (mmt) REVERT: N 515 TYR cc_start: 0.5232 (m-80) cc_final: 0.5004 (m-80) REVERT: N 525 GLN cc_start: 0.6794 (tp40) cc_final: 0.6502 (tp40) REVERT: N 543 ARG cc_start: 0.6637 (mtp85) cc_final: 0.6300 (mtp85) REVERT: N 598 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6256 (mt) REVERT: N 606 LEU cc_start: 0.6793 (tt) cc_final: 0.6451 (mt) REVERT: O 47 GLU cc_start: 0.6963 (tp30) cc_final: 0.6488 (tt0) REVERT: S 47 GLU cc_start: 0.5832 (mt-10) cc_final: 0.5521 (tt0) REVERT: U 79 ARG cc_start: 0.6427 (mmt180) cc_final: 0.6121 (mmt180) REVERT: X 64 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7730 (p) REVERT: Y 47 GLU cc_start: 0.7989 (tp30) cc_final: 0.7589 (tp30) REVERT: Z 47 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: M 29 LEU cc_start: 0.8222 (tp) cc_final: 0.7944 (tp) REVERT: M 59 ARG cc_start: 0.6777 (ttp-170) cc_final: 0.6325 (ttp-110) REVERT: M 65 GLN cc_start: 0.8273 (mt0) cc_final: 0.8027 (mm-40) REVERT: M 67 LYS cc_start: 0.7893 (mtpm) cc_final: 0.7289 (ptpt) REVERT: M 71 ASP cc_start: 0.8098 (p0) cc_final: 0.7645 (p0) REVERT: M 126 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6606 (mm-40) REVERT: M 291 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7576 (mmpt) REVERT: M 301 ARG cc_start: 0.7197 (mmm160) cc_final: 0.6659 (ttt90) REVERT: M 306 ARG cc_start: 0.7048 (tmm160) cc_final: 0.6683 (ttp-110) outliers start: 48 outliers final: 17 residues processed: 180 average time/residue: 1.6727 time to fit residues: 330.0902 Evaluate side-chains 160 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 237 HIS Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 598 LEU Chi-restraints excluded: chain N residue 638 ASN 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 X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 159 GLN Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 234 MET Chi-restraints excluded: chain M residue 291 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14133 Z= 0.282 Angle : 0.594 7.756 19120 Z= 0.299 Chirality : 0.040 0.155 2258 Planarity : 0.005 0.063 2459 Dihedral : 4.871 77.656 2032 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.10 % Allowed : 14.69 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 1863 helix: 1.76 (0.13), residues: 1440 sheet: -2.02 (0.66), residues: 48 loop : 0.05 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 295 HIS 0.006 0.001 HIS N 557 PHE 0.017 0.001 PHE M 172 TYR 0.016 0.001 TYR N 43 ARG 0.008 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.556 Fit side-chains REVERT: N 22 GLN cc_start: 0.6001 (OUTLIER) cc_final: 0.5109 (mp10) REVERT: N 50 ARG cc_start: 0.6171 (mtt90) cc_final: 0.5639 (mtp85) REVERT: N 54 ARG cc_start: 0.6095 (mpt90) cc_final: 0.5557 (mtm110) REVERT: N 75 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6858 (pt0) REVERT: N 155 GLU cc_start: 0.6420 (tt0) cc_final: 0.5775 (tm-30) REVERT: N 159 LYS cc_start: 0.6802 (mtmt) cc_final: 0.6597 (tmtm) REVERT: N 215 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6355 (tm-30) REVERT: N 218 ARG cc_start: 0.7292 (ttp80) cc_final: 0.6866 (mtm110) REVERT: N 233 GLU cc_start: 0.6673 (tp30) cc_final: 0.5981 (mt-10) REVERT: N 237 HIS cc_start: 0.6903 (OUTLIER) cc_final: 0.6634 (m-70) REVERT: N 306 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6261 (mm-30) REVERT: N 311 HIS cc_start: 0.5563 (m90) cc_final: 0.4586 (t70) REVERT: N 401 GLN cc_start: 0.7124 (tt0) cc_final: 0.6313 (mp10) REVERT: N 446 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7018 (mp) REVERT: N 453 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7205 (ttp-170) REVERT: N 484 TYR cc_start: 0.7158 (t80) cc_final: 0.6902 (t80) REVERT: N 490 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6241 (mpp-170) REVERT: N 515 TYR cc_start: 0.5232 (m-80) cc_final: 0.4995 (m-80) REVERT: N 525 GLN cc_start: 0.6816 (tp40) cc_final: 0.6559 (tp40) REVERT: N 543 ARG cc_start: 0.6674 (mtp85) cc_final: 0.6366 (mtp85) REVERT: N 606 LEU cc_start: 0.6845 (tt) cc_final: 0.6483 (mt) REVERT: O 47 GLU cc_start: 0.7185 (tp30) cc_final: 0.6750 (tt0) REVERT: S 47 GLU cc_start: 0.5884 (mt-10) cc_final: 0.5507 (tt0) REVERT: U 79 ARG cc_start: 0.6608 (mmt180) cc_final: 0.6280 (mmt180) REVERT: W 79 ARG cc_start: 0.6423 (mtt-85) cc_final: 0.6079 (mtp85) REVERT: Y 47 GLU cc_start: 0.8016 (tp30) cc_final: 0.7634 (tp30) REVERT: Z 47 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: M 59 ARG cc_start: 0.6802 (ttp-170) cc_final: 0.6326 (ttp-110) REVERT: M 71 ASP cc_start: 0.8174 (p0) cc_final: 0.7717 (p0) REVERT: M 126 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6811 (mm-40) REVERT: M 185 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6030 (mm-40) REVERT: M 301 ARG cc_start: 0.7302 (mmm160) cc_final: 0.6875 (ttm-80) REVERT: M 306 ARG cc_start: 0.7042 (tmm160) cc_final: 0.6699 (ttp-110) outliers start: 55 outliers final: 21 residues processed: 182 average time/residue: 1.5602 time to fit residues: 307.2054 Evaluate side-chains 163 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 LYS Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 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 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 490 ARG Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 54 THR 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 X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 185 GLN 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 59 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 M 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14133 Z= 0.320 Angle : 0.619 8.112 19120 Z= 0.311 Chirality : 0.041 0.156 2258 Planarity : 0.005 0.066 2459 Dihedral : 4.862 80.076 2028 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.10 % Allowed : 15.06 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 1863 helix: 1.69 (0.13), residues: 1440 sheet: -1.78 (0.69), residues: 48 loop : -0.16 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.006 0.001 HIS N 557 PHE 0.018 0.001 PHE M 172 TYR 0.023 0.002 TYR N 43 ARG 0.010 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: N 22 GLN cc_start: 0.6071 (OUTLIER) cc_final: 0.5153 (mp10) REVERT: N 54 ARG cc_start: 0.6171 (mpt90) cc_final: 0.5554 (mtm110) REVERT: N 66 THR cc_start: 0.7980 (t) cc_final: 0.7643 (m) REVERT: N 75 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6860 (pt0) REVERT: N 155 GLU cc_start: 0.6466 (tt0) cc_final: 0.5712 (tm-30) REVERT: N 215 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: N 218 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7105 (mtm110) REVERT: N 229 ARG cc_start: 0.6656 (mtm-85) cc_final: 0.6368 (mtt180) REVERT: N 233 GLU cc_start: 0.6674 (tp30) cc_final: 0.6030 (mt-10) REVERT: N 237 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6618 (m-70) REVERT: N 306 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6013 (tt0) REVERT: N 311 HIS cc_start: 0.5677 (m90) cc_final: 0.4709 (t70) REVERT: N 384 LYS cc_start: 0.6890 (tmmt) cc_final: 0.6667 (tttp) REVERT: N 401 GLN cc_start: 0.7151 (tt0) cc_final: 0.6314 (mp10) REVERT: N 446 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6975 (mp) REVERT: N 453 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7204 (ttp-170) REVERT: N 484 TYR cc_start: 0.7134 (t80) cc_final: 0.6865 (t80) REVERT: N 490 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6458 (mpp-170) REVERT: N 525 GLN cc_start: 0.6880 (tp40) cc_final: 0.6567 (tp40) REVERT: N 606 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6485 (mt) REVERT: Q 12 ARG cc_start: 0.5987 (mtp180) cc_final: 0.5574 (mtp85) REVERT: Q 49 ARG cc_start: 0.7354 (mtt180) cc_final: 0.7066 (mtp85) REVERT: S 47 GLU cc_start: 0.6023 (mt-10) cc_final: 0.5599 (tt0) REVERT: U 49 ARG cc_start: 0.7616 (mpt90) cc_final: 0.7008 (mmm160) REVERT: U 79 ARG cc_start: 0.6653 (mmt180) cc_final: 0.6324 (mmt180) REVERT: W 63 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7673 (mm-30) REVERT: W 79 ARG cc_start: 0.6477 (mtt-85) cc_final: 0.6138 (mtp85) REVERT: Y 47 GLU cc_start: 0.8060 (tp30) cc_final: 0.7677 (tp30) REVERT: Z 47 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: M 59 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6338 (ttp80) REVERT: M 67 LYS cc_start: 0.8043 (mtpm) cc_final: 0.7252 (ptpt) REVERT: M 71 ASP cc_start: 0.8172 (p0) cc_final: 0.7733 (p0) REVERT: M 185 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6190 (mm-40) REVERT: M 301 ARG cc_start: 0.7393 (mmm160) cc_final: 0.7013 (ttm-80) REVERT: M 306 ARG cc_start: 0.7097 (tmm160) cc_final: 0.6763 (ttp-110) outliers start: 55 outliers final: 23 residues processed: 181 average time/residue: 1.6004 time to fit residues: 312.4431 Evaluate side-chains 171 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 LYS Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 237 HIS Chi-restraints excluded: chain N residue 446 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 596 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 131 GLN Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 185 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 297 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14133 Z= 0.216 Angle : 0.540 8.361 19120 Z= 0.274 Chirality : 0.038 0.149 2258 Planarity : 0.005 0.058 2459 Dihedral : 4.677 80.360 2028 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.50 % Allowed : 16.11 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 1863 helix: 1.99 (0.13), residues: 1433 sheet: -1.64 (0.70), residues: 48 loop : -0.16 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 PHE 0.018 0.001 PHE N 427 TYR 0.019 0.001 TYR N 43 ARG 0.008 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6117 (mpt90) cc_final: 0.5548 (mtm110) REVERT: N 66 THR cc_start: 0.7968 (t) cc_final: 0.7692 (m) REVERT: N 75 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: N 155 GLU cc_start: 0.6492 (tt0) cc_final: 0.5744 (tm-30) REVERT: N 215 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: N 218 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7137 (mtm110) REVERT: N 237 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6630 (m-70) REVERT: N 306 GLU cc_start: 0.6383 (mt-10) cc_final: 0.5977 (tt0) REVERT: N 311 HIS cc_start: 0.5558 (m90) cc_final: 0.4650 (t70) REVERT: N 384 LYS cc_start: 0.6850 (tmmt) cc_final: 0.6613 (tttp) REVERT: N 401 GLN cc_start: 0.7001 (tt0) cc_final: 0.6184 (mp10) REVERT: N 446 LEU cc_start: 0.7495 (tp) cc_final: 0.7039 (OUTLIER) REVERT: N 453 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7223 (ttp-170) REVERT: N 484 TYR cc_start: 0.7147 (t80) cc_final: 0.6946 (t80) REVERT: N 525 GLN cc_start: 0.6836 (tp40) cc_final: 0.6625 (tp40) REVERT: N 543 ARG cc_start: 0.6669 (mtp85) cc_final: 0.6464 (mtp85) REVERT: N 606 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6480 (mt) REVERT: O 47 GLU cc_start: 0.7157 (tp30) cc_final: 0.6705 (tt0) REVERT: P 49 ARG cc_start: 0.7413 (mtp85) cc_final: 0.6799 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7240 (mtt180) cc_final: 0.6871 (mtp85) REVERT: U 79 ARG cc_start: 0.6553 (mmt180) cc_final: 0.6268 (mmt180) REVERT: W 79 ARG cc_start: 0.6513 (mtt-85) cc_final: 0.6197 (mtp85) REVERT: X 64 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7733 (p) REVERT: Y 47 GLU cc_start: 0.8002 (tp30) cc_final: 0.7655 (tp30) REVERT: Z 47 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: M 59 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6357 (ttp-110) REVERT: M 65 GLN cc_start: 0.8329 (mt0) cc_final: 0.8030 (mm-40) REVERT: M 67 LYS cc_start: 0.7957 (mtpm) cc_final: 0.7361 (ptpt) REVERT: M 71 ASP cc_start: 0.8132 (p0) cc_final: 0.7705 (p0) REVERT: M 126 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6945 (mm-40) REVERT: M 301 ARG cc_start: 0.7335 (mmm160) cc_final: 0.6965 (ttm-80) REVERT: M 306 ARG cc_start: 0.6997 (tmm160) cc_final: 0.6607 (ttp-110) outliers start: 47 outliers final: 17 residues processed: 177 average time/residue: 1.6765 time to fit residues: 320.2302 Evaluate side-chains 161 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 237 HIS Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU 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 X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 26 GLN M 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.7772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14133 Z= 0.189 Angle : 0.514 8.053 19120 Z= 0.263 Chirality : 0.037 0.162 2258 Planarity : 0.005 0.058 2459 Dihedral : 4.547 80.285 2028 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.76 % Allowed : 16.85 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.20), residues: 1863 helix: 2.16 (0.13), residues: 1436 sheet: -1.48 (0.71), residues: 48 loop : -0.16 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.004 0.001 HIS M 94 PHE 0.015 0.001 PHE N 427 TYR 0.016 0.001 TYR N 43 ARG 0.009 0.000 ARG X 12 *********************** 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 187 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6051 (mpt90) cc_final: 0.5495 (mtm110) REVERT: N 66 THR cc_start: 0.7954 (t) cc_final: 0.7688 (m) REVERT: N 75 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: N 155 GLU cc_start: 0.6488 (tt0) cc_final: 0.5777 (tm-30) REVERT: N 159 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6365 (tmtm) REVERT: N 215 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: N 218 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7208 (mtm110) REVERT: N 306 GLU cc_start: 0.6387 (mt-10) cc_final: 0.6092 (tt0) REVERT: N 311 HIS cc_start: 0.5478 (m90) cc_final: 0.4549 (t70) REVERT: N 384 LYS cc_start: 0.6835 (tmmt) cc_final: 0.6602 (tttp) REVERT: N 401 GLN cc_start: 0.6862 (tt0) cc_final: 0.6041 (mp10) REVERT: N 446 LEU cc_start: 0.7538 (tp) cc_final: 0.7091 (OUTLIER) REVERT: N 453 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7095 (ttp-170) REVERT: N 484 TYR cc_start: 0.7090 (t80) cc_final: 0.6861 (t80) REVERT: N 606 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6504 (mt) REVERT: O 47 GLU cc_start: 0.7146 (tp30) cc_final: 0.6695 (tt0) REVERT: P 49 ARG cc_start: 0.7329 (mtp85) cc_final: 0.6733 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7265 (mtt180) cc_final: 0.6871 (mtp85) REVERT: U 49 ARG cc_start: 0.7475 (mpt90) cc_final: 0.7008 (mmm160) REVERT: U 79 ARG cc_start: 0.6510 (mmt180) cc_final: 0.6263 (mmt180) REVERT: W 63 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7616 (mm-30) REVERT: W 79 ARG cc_start: 0.6456 (mtt-85) cc_final: 0.6189 (mtp85) REVERT: X 64 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7732 (p) REVERT: Y 47 GLU cc_start: 0.7974 (tp30) cc_final: 0.7657 (tp30) REVERT: Z 47 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: M 59 ARG cc_start: 0.6794 (ttp-170) cc_final: 0.6369 (ttp80) REVERT: M 65 GLN cc_start: 0.8304 (mt0) cc_final: 0.8009 (mm-40) REVERT: M 67 LYS cc_start: 0.7868 (mtpm) cc_final: 0.7347 (ptpt) REVERT: M 71 ASP cc_start: 0.8129 (p0) cc_final: 0.7693 (p0) REVERT: M 301 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6929 (ttm-80) REVERT: M 306 ARG cc_start: 0.6992 (tmm160) cc_final: 0.6594 (ttp-110) outliers start: 37 outliers final: 19 residues processed: 174 average time/residue: 1.7362 time to fit residues: 325.5248 Evaluate side-chains 170 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 75 GLU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 215 GLU Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 183 HIS M 26 GLN M 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.7814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14133 Z= 0.194 Angle : 0.519 8.215 19120 Z= 0.264 Chirality : 0.037 0.164 2258 Planarity : 0.005 0.055 2459 Dihedral : 4.518 80.482 2028 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.46 % Allowed : 17.82 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.19), residues: 1863 helix: 2.17 (0.13), residues: 1438 sheet: -1.34 (0.73), residues: 48 loop : -0.21 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 295 HIS 0.009 0.001 HIS N 183 PHE 0.015 0.001 PHE N 427 TYR 0.017 0.001 TYR N 43 ARG 0.009 0.000 ARG X 12 *********************** 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: 33 poor density : 147 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6010 (mpt90) cc_final: 0.5531 (mtm110) REVERT: N 66 THR cc_start: 0.7954 (t) cc_final: 0.7680 (m) REVERT: N 155 GLU cc_start: 0.6489 (tt0) cc_final: 0.5770 (tm-30) REVERT: N 183 HIS cc_start: 0.6616 (t-90) cc_final: 0.6316 (t70) REVERT: N 184 ARG cc_start: 0.6537 (ttp-110) cc_final: 0.6258 (ttp-110) REVERT: N 215 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6608 (tm-30) REVERT: N 218 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7190 (mtm110) REVERT: N 306 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6122 (tt0) REVERT: N 311 HIS cc_start: 0.5541 (m90) cc_final: 0.4588 (t70) REVERT: N 384 LYS cc_start: 0.6843 (tmmt) cc_final: 0.6608 (tttp) REVERT: N 401 GLN cc_start: 0.6862 (tt0) cc_final: 0.6038 (mp10) REVERT: N 453 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7078 (ttp-170) REVERT: N 484 TYR cc_start: 0.7111 (t80) cc_final: 0.6882 (t80) REVERT: N 606 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6504 (mt) REVERT: O 47 GLU cc_start: 0.7133 (tp30) cc_final: 0.6761 (tt0) REVERT: P 49 ARG cc_start: 0.7347 (mtp85) cc_final: 0.6732 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6941 (mtp85) REVERT: R 49 ARG cc_start: 0.7197 (mpt180) cc_final: 0.6875 (mmm160) REVERT: U 49 ARG cc_start: 0.7495 (mpt90) cc_final: 0.7078 (mmm160) REVERT: U 79 ARG cc_start: 0.6566 (mmt180) cc_final: 0.6321 (mmt180) REVERT: W 79 ARG cc_start: 0.6434 (mtt-85) cc_final: 0.6165 (mtp85) REVERT: X 64 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7732 (p) REVERT: Y 47 GLU cc_start: 0.7978 (tp30) cc_final: 0.7661 (tp30) REVERT: Z 47 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: M 59 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6264 (ttp80) REVERT: M 65 GLN cc_start: 0.8293 (mt0) cc_final: 0.7998 (mm-40) REVERT: M 67 LYS cc_start: 0.7885 (mtpm) cc_final: 0.7382 (ptpt) REVERT: M 71 ASP cc_start: 0.8139 (p0) cc_final: 0.7707 (p0) REVERT: M 301 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6830 (ttm-80) REVERT: M 306 ARG cc_start: 0.6970 (tmm160) cc_final: 0.6572 (ttp-110) outliers start: 33 outliers final: 17 residues processed: 169 average time/residue: 1.7628 time to fit residues: 320.1663 Evaluate side-chains 162 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 606 LEU 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 V residue 67 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 30.0000 chunk 168 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 26 GLN M 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.7863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14133 Z= 0.195 Angle : 0.517 8.294 19120 Z= 0.263 Chirality : 0.037 0.156 2258 Planarity : 0.005 0.056 2459 Dihedral : 4.501 80.466 2028 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.09 % Allowed : 18.12 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.20), residues: 1863 helix: 2.19 (0.13), residues: 1438 sheet: -1.33 (0.72), residues: 48 loop : -0.22 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 295 HIS 0.004 0.001 HIS M 94 PHE 0.014 0.001 PHE N 427 TYR 0.017 0.001 TYR N 43 ARG 0.009 0.000 ARG X 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 54 ARG cc_start: 0.6159 (mpt90) cc_final: 0.5593 (mtm110) REVERT: N 66 THR cc_start: 0.7957 (t) cc_final: 0.7677 (m) REVERT: N 139 ARG cc_start: 0.6037 (tpt170) cc_final: 0.5738 (mmm160) REVERT: N 155 GLU cc_start: 0.6570 (tt0) cc_final: 0.5857 (tm-30) REVERT: N 179 LEU cc_start: 0.7239 (tt) cc_final: 0.6956 (mt) REVERT: N 183 HIS cc_start: 0.6561 (t-90) cc_final: 0.6239 (t70) REVERT: N 184 ARG cc_start: 0.6592 (ttp-110) cc_final: 0.6293 (ttp-110) REVERT: N 218 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7233 (mtm110) REVERT: N 306 GLU cc_start: 0.6364 (mt-10) cc_final: 0.6107 (tt0) REVERT: N 311 HIS cc_start: 0.5581 (m90) cc_final: 0.4608 (t70) REVERT: N 384 LYS cc_start: 0.6849 (tmmt) cc_final: 0.6610 (tttp) REVERT: N 401 GLN cc_start: 0.6863 (tt0) cc_final: 0.6037 (mp10) REVERT: N 453 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7081 (ttp-170) REVERT: N 484 TYR cc_start: 0.7111 (t80) cc_final: 0.6879 (t80) REVERT: N 606 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6503 (mt) REVERT: O 47 GLU cc_start: 0.7236 (tp30) cc_final: 0.6860 (tt0) REVERT: P 49 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6735 (mmt-90) REVERT: Q 49 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6939 (mtp85) REVERT: R 49 ARG cc_start: 0.7162 (mpt180) cc_final: 0.6876 (mmm160) REVERT: U 49 ARG cc_start: 0.7467 (mpt90) cc_final: 0.7018 (mmm160) REVERT: U 79 ARG cc_start: 0.6651 (mmt180) cc_final: 0.6411 (mmt180) REVERT: W 63 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7674 (mm-30) REVERT: W 79 ARG cc_start: 0.6496 (mtt-85) cc_final: 0.6210 (mtp85) REVERT: X 64 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7733 (p) REVERT: Y 47 GLU cc_start: 0.7972 (tp30) cc_final: 0.7657 (tp30) REVERT: Z 47 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: M 59 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6269 (ttp80) REVERT: M 65 GLN cc_start: 0.8306 (mt0) cc_final: 0.8003 (mm-40) REVERT: M 67 LYS cc_start: 0.7920 (mtpm) cc_final: 0.7435 (ptpt) REVERT: M 71 ASP cc_start: 0.8129 (p0) cc_final: 0.7702 (p0) REVERT: M 301 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6823 (ttm-80) REVERT: M 306 ARG cc_start: 0.6976 (tmm160) cc_final: 0.6554 (ttp-110) outliers start: 28 outliers final: 18 residues processed: 163 average time/residue: 1.7571 time to fit residues: 308.1628 Evaluate side-chains 167 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 145 LEU Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 204 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 453 ARG Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 490 ARG Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 595 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 638 ASN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 26 GLN M 94 HIS M 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104007 restraints weight = 14172.965| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.64 r_work: 0.3083 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.7893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14133 Z= 0.243 Angle : 0.553 8.174 19120 Z= 0.280 Chirality : 0.039 0.159 2258 Planarity : 0.005 0.057 2459 Dihedral : 4.573 80.481 2028 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.01 % Allowed : 18.20 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 1863 helix: 2.05 (0.13), residues: 1438 sheet: -1.38 (0.71), residues: 48 loop : -0.33 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 295 HIS 0.005 0.001 HIS M 94 PHE 0.015 0.001 PHE M 172 TYR 0.020 0.001 TYR N 43 ARG 0.009 0.000 ARG X 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5325.68 seconds wall clock time: 96 minutes 0.71 seconds (5760.71 seconds total)