Starting phenix.real_space_refine on Sun Feb 18 04:52:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/02_2024/7jz6_22530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/02_2024/7jz6_22530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/02_2024/7jz6_22530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/02_2024/7jz6_22530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/02_2024/7jz6_22530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz6_22530/02_2024/7jz6_22530_updated.pdb" } resolution = 2.53 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.360 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 44 5.16 5 C 13258 2.51 5 N 3589 2.21 5 O 3947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 508": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 650": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B GLU 695": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 608": "OE1" <-> "OE2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ARG 650": "NH1" <-> "NH2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C ARG 722": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 381": "NH1" <-> "NH2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 421": "NH1" <-> "NH2" Residue "D GLU 447": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D GLU 567": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D ARG 583": "NH1" <-> "NH2" Residue "D ARG 585": "NH1" <-> "NH2" Residue "D GLU 592": "OE1" <-> "OE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 650": "NH1" <-> "NH2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D ARG 666": "NH1" <-> "NH2" Residue "D ARG 668": "NH1" <-> "NH2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D GLU 695": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D ARG 722": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5154 Classifications: {'peptide': 660} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "C" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "D" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 10.77, per 1000 atoms: 0.52 Number of scatterers: 20842 At special positions: 0 Unit cell: (126.36, 98.28, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 44 16.00 O 3947 8.00 N 3589 7.00 C 13258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.29 Conformation dependent library (CDL) restraints added in 3.8 seconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 9 sheets defined 47.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.928A pdb=" N LYS A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 removed outlier: 4.148A pdb=" N THR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.637A pdb=" N ARG A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 139 through 156 removed outlier: 3.820A pdb=" N LEU A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Proline residue: A 148 - end of helix removed outlier: 6.731A pdb=" N GLN A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 4.165A pdb=" N ILE A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.733A pdb=" N MET A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 375 through 382 removed outlier: 4.441A pdb=" N LEU A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.931A pdb=" N LYS A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 506 through 519 Proline residue: A 511 - end of helix removed outlier: 3.843A pdb=" N GLU A 514 " --> pdb=" O PRO A 511 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 519 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 543 removed outlier: 3.663A pdb=" N GLY A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 566 through 572 removed outlier: 4.002A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 606 through 618 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 641 through 647 Processing helix chain 'A' and resid 679 through 685 removed outlier: 5.164A pdb=" N PHE A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLY A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.662A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 719 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.937A pdb=" N LYS B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 removed outlier: 4.139A pdb=" N THR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.523A pdb=" N ARG B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 110 " --> pdb=" O HIS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 139 through 156 removed outlier: 3.806A pdb=" N LEU B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TRP B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Proline residue: B 148 - end of helix removed outlier: 6.722A pdb=" N GLN B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 4.158A pdb=" N ILE B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.609A pdb=" N ALA B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 328 through 335 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.950A pdb=" N LYS B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 413 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 464 through 475 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 506 through 519 Proline residue: B 511 - end of helix removed outlier: 3.831A pdb=" N GLU B 514 " --> pdb=" O PRO B 511 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU B 519 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 543 removed outlier: 3.666A pdb=" N GLY B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 566 through 572 removed outlier: 4.000A pdb=" N LEU B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 591 through 601 Processing helix chain 'B' and resid 606 through 618 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 641 through 647 Processing helix chain 'B' and resid 679 through 685 removed outlier: 5.147A pdb=" N PHE B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLY B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.665A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 719 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 62 through 68 removed outlier: 4.011A pdb=" N LYS C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 83 removed outlier: 4.151A pdb=" N THR C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 97 through 110 removed outlier: 3.606A pdb=" N ARG C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR C 110 " --> pdb=" O HIS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 139 through 156 removed outlier: 3.813A pdb=" N LEU C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TRP C 147 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Proline residue: C 148 - end of helix removed outlier: 6.728A pdb=" N GLN C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 172 removed outlier: 4.148A pdb=" N ILE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.574A pdb=" N MET C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 328 through 335 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 384 through 394 removed outlier: 3.990A pdb=" N LYS C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 413 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 433 through 435 No H-bonds generated for 'chain 'C' and resid 433 through 435' Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 464 through 477 removed outlier: 5.122A pdb=" N THR C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing helix chain 'C' and resid 501 through 503 No H-bonds generated for 'chain 'C' and resid 501 through 503' Processing helix chain 'C' and resid 506 through 519 Proline residue: C 511 - end of helix removed outlier: 3.825A pdb=" N GLU C 514 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU C 519 " --> pdb=" O ILE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 544 removed outlier: 3.683A pdb=" N GLY C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 563 No H-bonds generated for 'chain 'C' and resid 561 through 563' Processing helix chain 'C' and resid 566 through 572 removed outlier: 4.062A pdb=" N LEU C 571 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 580 No H-bonds generated for 'chain 'C' and resid 578 through 580' Processing helix chain 'C' and resid 591 through 601 Processing helix chain 'C' and resid 606 through 618 Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 641 through 647 Processing helix chain 'C' and resid 679 through 685 removed outlier: 5.180A pdb=" N PHE C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY C 685 " --> pdb=" O ASP C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 698 removed outlier: 3.661A pdb=" N VAL C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 719 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.857A pdb=" N LYS D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 removed outlier: 4.164A pdb=" N THR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 97 through 110 removed outlier: 3.610A pdb=" N ARG D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 139 through 156 removed outlier: 3.821A pdb=" N LEU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Proline residue: D 148 - end of helix removed outlier: 6.740A pdb=" N GLN D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYS D 156 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 4.158A pdb=" N ILE D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 240 through 252 removed outlier: 3.591A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 249 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 375 through 381 removed outlier: 4.309A pdb=" N LEU D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.947A pdb=" N LYS D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 447 through 460 Processing helix chain 'D' and resid 464 through 477 removed outlier: 5.143A pdb=" N THR D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 501 through 503 No H-bonds generated for 'chain 'D' and resid 501 through 503' Processing helix chain 'D' and resid 506 through 519 Proline residue: D 511 - end of helix removed outlier: 3.839A pdb=" N GLU D 514 " --> pdb=" O PRO D 511 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU D 519 " --> pdb=" O ILE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 543 removed outlier: 3.696A pdb=" N GLY D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 566 through 572 removed outlier: 4.157A pdb=" N LEU D 571 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 572 " --> pdb=" O MET D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 580 No H-bonds generated for 'chain 'D' and resid 578 through 580' Processing helix chain 'D' and resid 591 through 601 Processing helix chain 'D' and resid 606 through 618 Processing helix chain 'D' and resid 623 through 625 No H-bonds generated for 'chain 'D' and resid 623 through 625' Processing helix chain 'D' and resid 641 through 647 Processing helix chain 'D' and resid 679 through 685 removed outlier: 5.176A pdb=" N PHE D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY D 685 " --> pdb=" O ASP D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 removed outlier: 3.663A pdb=" N VAL D 693 " --> pdb=" O VAL D 689 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 719 Processing sheet with id= A, first strand: chain 'A' and resid 338 through 342 Processing sheet with id= B, first strand: chain 'A' and resid 651 through 655 removed outlier: 3.512A pdb=" N PHE A 675 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP A 667 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 673 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 337 through 343 removed outlier: 4.679A pdb=" N GLU B 337 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.538A pdb=" N PHE B 675 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 667 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 673 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 337 through 342 removed outlier: 4.757A pdb=" N GLU C 337 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 353 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 651 through 655 removed outlier: 7.132A pdb=" N ASP C 667 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 673 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.629A pdb=" N ASP C 361 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS C 367 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 339 through 342 Processing sheet with id= I, first strand: chain 'D' and resid 651 through 655 removed outlier: 3.648A pdb=" N PHE D 675 " --> pdb=" O GLY D 665 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP D 667 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL D 673 " --> pdb=" O ASP D 667 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1788 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: 6.21 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.33: 4661 1.33 - 1.52: 10007 1.52 - 1.70: 6596 1.70 - 1.89: 88 1.89 - 2.08: 16 Bond restraints: 21368 Sorted by residual: bond pdb=" C VAL C 227 " pdb=" O VAL C 227 " ideal model delta sigma weight residual 1.233 1.138 0.095 1.08e-02 8.57e+03 7.69e+01 bond pdb=" C VAL B 227 " pdb=" O VAL B 227 " ideal model delta sigma weight residual 1.233 1.144 0.089 1.08e-02 8.57e+03 6.78e+01 bond pdb=" C TRP C 89 " pdb=" O TRP C 89 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.28e-02 6.10e+03 3.37e+01 bond pdb=" CA PRO C 90 " pdb=" C PRO C 90 " ideal model delta sigma weight residual 1.521 1.582 -0.061 1.27e-02 6.20e+03 2.32e+01 bond pdb=" C ASN A 280 " pdb=" O ASN A 280 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.29e-02 6.01e+03 2.02e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 88.67 - 106.45: 679 106.45 - 124.24: 27555 124.24 - 142.02: 826 142.02 - 159.80: 0 159.80 - 177.58: 8 Bond angle restraints: 29068 Sorted by residual: angle pdb=" N VAL B 588 " pdb=" CA VAL B 588 " pdb=" C VAL B 588 " ideal model delta sigma weight residual 110.53 126.23 -15.70 9.40e-01 1.13e+00 2.79e+02 angle pdb=" N ILE D 225 " pdb=" CA ILE D 225 " pdb=" C ILE D 225 " ideal model delta sigma weight residual 110.53 123.63 -13.10 9.40e-01 1.13e+00 1.94e+02 angle pdb=" N GLY C 270 " pdb=" CA GLY C 270 " pdb=" C GLY C 270 " ideal model delta sigma weight residual 111.02 127.58 -16.56 1.86e+00 2.89e-01 7.93e+01 angle pdb=" N GLY B 270 " pdb=" CA GLY B 270 " pdb=" C GLY B 270 " ideal model delta sigma weight residual 111.02 127.14 -16.12 1.86e+00 2.89e-01 7.51e+01 angle pdb=" N VAL D 316 " pdb=" CA VAL D 316 " pdb=" C VAL D 316 " ideal model delta sigma weight residual 108.11 119.44 -11.33 1.40e+00 5.10e-01 6.55e+01 ... (remaining 29063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10623 17.84 - 35.68: 1297 35.68 - 53.52: 447 53.52 - 71.36: 141 71.36 - 89.21: 42 Dihedral angle restraints: 12550 sinusoidal: 5022 harmonic: 7528 Sorted by residual: dihedral pdb=" C VAL B 588 " pdb=" N VAL B 588 " pdb=" CA VAL B 588 " pdb=" CB VAL B 588 " ideal model delta harmonic sigma weight residual -122.00 -136.41 14.41 0 2.50e+00 1.60e-01 3.32e+01 dihedral pdb=" C GLU D 315 " pdb=" N GLU D 315 " pdb=" CA GLU D 315 " pdb=" CB GLU D 315 " ideal model delta harmonic sigma weight residual -122.60 -134.81 12.21 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" CA ASP D 44 " pdb=" C ASP D 44 " pdb=" N LEU D 45 " pdb=" CA LEU D 45 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 12547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.360: 3031 0.360 - 0.719: 12 0.719 - 1.079: 0 1.079 - 1.438: 1 1.438 - 1.798: 7 Chirality restraints: 3051 Sorted by residual: chirality pdb=" CG LEU A 662 " pdb=" CB LEU A 662 " pdb=" CD1 LEU A 662 " pdb=" CD2 LEU A 662 " both_signs ideal model delta sigma weight residual False -2.59 -0.79 -1.80 2.00e-01 2.50e+01 8.08e+01 chirality pdb=" CG LEU B 139 " pdb=" CB LEU B 139 " pdb=" CD1 LEU B 139 " pdb=" CD2 LEU B 139 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.68e+01 chirality pdb=" CG LEU A 193 " pdb=" CB LEU A 193 " pdb=" CD1 LEU A 193 " pdb=" CD2 LEU A 193 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.67e+01 ... (remaining 3048 not shown) Planarity restraints: 3825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 89 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO C 90 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 89 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 90 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 89 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO D 90 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " 0.044 5.00e-02 4.00e+02 ... (remaining 3822 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 8 1.96 - 2.69: 785 2.69 - 3.43: 30095 3.43 - 4.16: 52702 4.16 - 4.90: 91792 Nonbonded interactions: 175382 Sorted by model distance: nonbonded pdb=" CH2 TRP D 105 " pdb=" CE2 TYR D 226 " model vdw 1.219 3.640 nonbonded pdb=" CH2 TRP B 105 " pdb=" CE2 TYR B 226 " model vdw 1.296 3.640 nonbonded pdb=" CH2 TRP C 105 " pdb=" CE2 TYR C 226 " model vdw 1.310 3.640 nonbonded pdb=" CH2 TRP A 105 " pdb=" CE2 TYR A 226 " model vdw 1.357 3.640 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLN A 324 " model vdw 1.865 2.440 ... (remaining 175377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 38 through 195 or resid 224 through 725 or resid 1001)) selection = (chain 'C' and (resid 38 through 195 or resid 224 through 725 or resid 1001)) selection = (chain 'D' and (resid 38 through 195 or resid 224 through 725 or resid 1001)) } 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: 0.090 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: 1.700 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 55.170 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.130 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 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 : 0.009 0.132 21368 Z= 0.571 Angle : 1.038 16.560 29068 Z= 0.598 Chirality : 0.106 1.798 3051 Planarity : 0.007 0.097 3825 Dihedral : 19.126 89.205 7720 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 11.17 % Allowed : 17.34 % Favored : 71.48 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 5.56 % 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: -3.03 (0.14), residues: 2630 helix: -1.92 (0.12), residues: 1108 sheet: -0.37 (0.56), residues: 78 loop : -2.21 (0.14), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP C 88 HIS 0.013 0.004 HIS C 49 PHE 0.029 0.004 PHE B 675 TYR 0.037 0.004 TYR C 226 ARG 0.010 0.001 ARG D 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 387 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4657 (pm20) REVERT: A 141 LYS cc_start: 0.7726 (mttp) cc_final: 0.7519 (mttp) REVERT: A 144 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6905 (tpp-160) REVERT: A 358 ILE cc_start: 0.5856 (OUTLIER) cc_final: 0.5558 (pt) REVERT: A 396 ASP cc_start: 0.5786 (OUTLIER) cc_final: 0.5479 (t0) REVERT: A 414 ARG cc_start: 0.7162 (ptt180) cc_final: 0.6685 (ptt180) REVERT: A 421 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7319 (mtp-110) REVERT: A 454 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7418 (mtpm) REVERT: A 522 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6661 (mptp) REVERT: A 581 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.7086 (t0) REVERT: A 623 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6480 (p90) REVERT: A 708 LYS cc_start: 0.7376 (mtmt) cc_final: 0.7097 (mptt) REVERT: B 68 LYS cc_start: 0.7524 (mttt) cc_final: 0.7291 (mttm) REVERT: B 144 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6892 (tpp-160) REVERT: B 156 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6932 (ttmt) REVERT: B 286 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5514 (mm-30) REVERT: B 381 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5418 (tpt-90) REVERT: B 414 ARG cc_start: 0.7174 (ptt180) cc_final: 0.6755 (ptt180) REVERT: B 452 ASP cc_start: 0.6558 (m-30) cc_final: 0.5869 (t0) REVERT: B 454 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7336 (mtpm) REVERT: B 522 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6535 (mptp) REVERT: B 623 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6210 (p90) REVERT: C 42 ARG cc_start: 0.6024 (mmm-85) cc_final: 0.5780 (mmt90) REVERT: C 144 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6819 (tpp-160) REVERT: C 156 LYS cc_start: 0.7270 (mtmm) cc_final: 0.6783 (mtmt) REVERT: C 414 ARG cc_start: 0.7020 (ptt180) cc_final: 0.6613 (ptt180) REVERT: C 571 LEU cc_start: 0.6996 (mt) cc_final: 0.6754 (mt) REVERT: C 575 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6430 (mm) REVERT: C 623 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.6126 (p90) REVERT: C 648 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6384 (t0) REVERT: C 667 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5069 (t0) REVERT: C 705 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6535 (tttm) REVERT: C 708 LYS cc_start: 0.7327 (mtmt) cc_final: 0.7051 (tptp) REVERT: D 42 ARG cc_start: 0.6065 (mmm-85) cc_final: 0.5850 (mmt90) REVERT: D 58 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.4523 (pm20) REVERT: D 64 LYS cc_start: 0.6128 (ttmm) cc_final: 0.5837 (ttmm) REVERT: D 68 LYS cc_start: 0.7370 (mttt) cc_final: 0.7128 (mttm) REVERT: D 103 MET cc_start: 0.7448 (ttp) cc_final: 0.7208 (ttm) REVERT: D 133 TRP cc_start: 0.5721 (m-10) cc_final: 0.5461 (m-10) REVERT: D 144 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6928 (tpp-160) REVERT: D 299 SER cc_start: 0.5310 (OUTLIER) cc_final: 0.4998 (t) REVERT: D 414 ARG cc_start: 0.7232 (ptt180) cc_final: 0.6877 (ptt180) REVERT: D 539 LYS cc_start: 0.6850 (tttp) cc_final: 0.6518 (mtpp) REVERT: D 565 ASP cc_start: 0.6420 (t70) cc_final: 0.6054 (t0) REVERT: D 623 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6161 (p90) REVERT: D 666 ARG cc_start: 0.5233 (OUTLIER) cc_final: 0.4811 (ptp-170) REVERT: D 674 LYS cc_start: 0.7039 (tttp) cc_final: 0.6702 (tttm) REVERT: D 705 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6251 (tttt) REVERT: D 708 LYS cc_start: 0.7275 (mtmt) cc_final: 0.7059 (mptt) outliers start: 239 outliers final: 156 residues processed: 585 average time/residue: 1.4569 time to fit residues: 951.6287 Evaluate side-chains 550 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 366 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain D residue 666 ARG Chi-restraints excluded: chain D residue 668 ARG Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 686 SER Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain D residue 705 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 125 GLN B 645 ASN C 628 ASN C 645 ASN D 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21368 Z= 0.284 Angle : 0.696 13.970 29068 Z= 0.358 Chirality : 0.045 0.161 3051 Planarity : 0.006 0.062 3825 Dihedral : 13.236 93.749 3289 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 7.76 % Allowed : 20.66 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.39 (0.15), residues: 2630 helix: -0.53 (0.14), residues: 1076 sheet: 0.00 (0.54), residues: 78 loop : -1.26 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 338 HIS 0.013 0.002 HIS B 49 PHE 0.020 0.003 PHE A 675 TYR 0.019 0.002 TYR B 226 ARG 0.006 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 382 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.4829 (OUTLIER) cc_final: 0.3848 (pm20) REVERT: A 64 LYS cc_start: 0.6171 (mtpm) cc_final: 0.5958 (ttmm) REVERT: A 144 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6963 (tpp-160) REVERT: A 156 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6791 (mtmt) REVERT: A 396 ASP cc_start: 0.5726 (OUTLIER) cc_final: 0.5496 (t0) REVERT: A 414 ARG cc_start: 0.7000 (ptt180) cc_final: 0.6482 (ptt180) REVERT: A 421 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7502 (mtp-110) REVERT: A 433 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6809 (tp) REVERT: A 454 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7207 (mtpm) REVERT: A 479 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6868 (mtp180) REVERT: A 580 ARG cc_start: 0.7675 (ptt180) cc_final: 0.7312 (ptm160) REVERT: A 581 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7120 (t0) REVERT: A 623 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6090 (p90) REVERT: A 708 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6944 (tptp) REVERT: B 144 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6940 (tpp-160) REVERT: B 156 LYS cc_start: 0.7296 (mtmm) cc_final: 0.6847 (mtmt) REVERT: B 299 SER cc_start: 0.5005 (OUTLIER) cc_final: 0.4693 (t) REVERT: B 336 TYR cc_start: 0.5495 (m-80) cc_final: 0.5250 (m-80) REVERT: B 433 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6536 (tp) REVERT: B 452 ASP cc_start: 0.6661 (m-30) cc_final: 0.6001 (t0) REVERT: B 454 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7387 (mtmm) REVERT: B 522 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6578 (mptp) REVERT: B 623 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.5764 (p90) REVERT: C 42 ARG cc_start: 0.5908 (mmm-85) cc_final: 0.5662 (mmt90) REVERT: C 64 LYS cc_start: 0.6064 (ttmm) cc_final: 0.5831 (ttmm) REVERT: C 76 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6563 (tmtt) REVERT: C 144 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6887 (tpp-160) REVERT: C 156 LYS cc_start: 0.7304 (mtmm) cc_final: 0.6812 (mtmt) REVERT: C 299 SER cc_start: 0.5424 (OUTLIER) cc_final: 0.5184 (t) REVERT: C 342 ARG cc_start: 0.5066 (OUTLIER) cc_final: 0.4579 (mmm160) REVERT: C 571 LEU cc_start: 0.7038 (mt) cc_final: 0.6811 (mt) REVERT: C 575 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6324 (mm) REVERT: C 581 ASN cc_start: 0.7060 (t0) cc_final: 0.6769 (t0) REVERT: C 623 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.5809 (p90) REVERT: C 708 LYS cc_start: 0.7251 (mtmt) cc_final: 0.6927 (mmtt) REVERT: D 68 LYS cc_start: 0.7147 (mttt) cc_final: 0.6885 (mttm) REVERT: D 79 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6538 (ttpt) REVERT: D 133 TRP cc_start: 0.5655 (m-10) cc_final: 0.5422 (m-10) REVERT: D 144 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6839 (tpp-160) REVERT: D 163 PHE cc_start: 0.7632 (m-80) cc_final: 0.7401 (m-80) REVERT: D 299 SER cc_start: 0.5418 (OUTLIER) cc_final: 0.5089 (t) REVERT: D 479 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6971 (mtp180) REVERT: D 539 LYS cc_start: 0.6787 (tttp) cc_final: 0.6421 (mtpp) REVERT: D 623 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5687 (p90) REVERT: D 674 LYS cc_start: 0.7123 (tttp) cc_final: 0.6670 (tttm) REVERT: D 708 LYS cc_start: 0.7135 (mtmt) cc_final: 0.6751 (mmtt) outliers start: 166 outliers final: 97 residues processed: 510 average time/residue: 1.4432 time to fit residues: 823.7407 Evaluate side-chains 492 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 369 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 199 optimal weight: 0.0670 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 81 optimal weight: 0.0870 chunk 192 optimal weight: 0.9990 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21368 Z= 0.184 Angle : 0.574 11.870 29068 Z= 0.292 Chirality : 0.041 0.159 3051 Planarity : 0.005 0.050 3825 Dihedral : 10.676 76.935 3110 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.89 % Allowed : 22.53 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.40 (0.16), residues: 2630 helix: 0.32 (0.15), residues: 1072 sheet: -0.08 (0.53), residues: 88 loop : -0.68 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 338 HIS 0.006 0.001 HIS B 49 PHE 0.014 0.002 PHE B 675 TYR 0.012 0.002 TYR D 226 ARG 0.004 0.000 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 374 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.6518 (tp30) cc_final: 0.6125 (tp30) REVERT: A 144 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6944 (tpp-160) REVERT: A 156 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6803 (mtmt) REVERT: A 163 PHE cc_start: 0.7840 (m-80) cc_final: 0.7574 (m-80) REVERT: A 310 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5526 (mm) REVERT: A 317 VAL cc_start: 0.6641 (t) cc_final: 0.6252 (p) REVERT: A 421 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7396 (mtp-110) REVERT: A 448 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6977 (tp40) REVERT: A 454 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7486 (mtmm) REVERT: A 479 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6952 (mtp180) REVERT: A 580 ARG cc_start: 0.7658 (ptt180) cc_final: 0.7331 (ptm160) REVERT: A 598 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.6810 (tmtp) REVERT: A 623 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6341 (p90) REVERT: A 708 LYS cc_start: 0.7202 (mtmt) cc_final: 0.6919 (tptp) REVERT: B 75 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6467 (mttp) REVERT: B 112 ARG cc_start: 0.6664 (mtp180) cc_final: 0.6391 (mtm110) REVERT: B 144 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6800 (tpp-160) REVERT: B 156 LYS cc_start: 0.7196 (mtmm) cc_final: 0.6792 (mtmt) REVERT: B 194 ASP cc_start: 0.2678 (OUTLIER) cc_final: 0.2353 (p0) REVERT: B 433 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6556 (tp) REVERT: B 448 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6969 (tp40) REVERT: B 452 ASP cc_start: 0.6573 (m-30) cc_final: 0.6054 (t70) REVERT: B 479 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6678 (mtp180) REVERT: B 581 ASN cc_start: 0.7142 (t0) cc_final: 0.6669 (t0) REVERT: B 623 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6111 (p90) REVERT: B 674 LYS cc_start: 0.7197 (tttp) cc_final: 0.6949 (tttm) REVERT: C 144 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6859 (tpp-160) REVERT: C 156 LYS cc_start: 0.7307 (mtmm) cc_final: 0.6860 (mtmt) REVERT: C 317 VAL cc_start: 0.6561 (t) cc_final: 0.6239 (p) REVERT: C 359 ILE cc_start: 0.5219 (OUTLIER) cc_final: 0.4847 (mp) REVERT: C 414 ARG cc_start: 0.7092 (ptt180) cc_final: 0.6788 (ptt180) REVERT: C 448 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6674 (tp40) REVERT: C 479 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6971 (mtp180) REVERT: C 571 LEU cc_start: 0.7095 (mt) cc_final: 0.6813 (mt) REVERT: C 575 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6154 (mm) REVERT: C 598 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.6712 (tmtp) REVERT: C 708 LYS cc_start: 0.7190 (mtmt) cc_final: 0.6820 (mmtt) REVERT: D 64 LYS cc_start: 0.5957 (ttmm) cc_final: 0.5728 (mtpp) REVERT: D 133 TRP cc_start: 0.5623 (m-10) cc_final: 0.5383 (m-10) REVERT: D 144 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6858 (tpp-160) REVERT: D 156 LYS cc_start: 0.7527 (mtmp) cc_final: 0.7018 (mtmt) REVERT: D 163 PHE cc_start: 0.7579 (m-80) cc_final: 0.7373 (m-80) REVERT: D 299 SER cc_start: 0.5118 (OUTLIER) cc_final: 0.4888 (t) REVERT: D 414 ARG cc_start: 0.7090 (ptt180) cc_final: 0.6800 (ptt180) REVERT: D 448 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6840 (tp40) REVERT: D 452 ASP cc_start: 0.6433 (m-30) cc_final: 0.5985 (t70) REVERT: D 479 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7049 (mtp180) REVERT: D 539 LYS cc_start: 0.6756 (tttp) cc_final: 0.6317 (mtpp) REVERT: D 565 ASP cc_start: 0.6295 (t70) cc_final: 0.5904 (t0) REVERT: D 598 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.6732 (tmtp) REVERT: D 623 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.6147 (p90) REVERT: D 674 LYS cc_start: 0.7105 (tttp) cc_final: 0.6696 (tttm) REVERT: D 708 LYS cc_start: 0.7112 (mtmt) cc_final: 0.6733 (mmtt) outliers start: 126 outliers final: 52 residues processed: 478 average time/residue: 1.5233 time to fit residues: 812.3811 Evaluate side-chains 447 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 368 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN D 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 21368 Z= 0.383 Angle : 0.770 14.371 29068 Z= 0.399 Chirality : 0.049 0.194 3051 Planarity : 0.007 0.054 3825 Dihedral : 10.800 89.777 3030 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.55 % Allowed : 22.25 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.74 (0.15), residues: 2630 helix: -0.06 (0.14), residues: 1080 sheet: 0.27 (0.56), residues: 78 loop : -0.82 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 338 HIS 0.011 0.003 HIS C 49 PHE 0.020 0.003 PHE A 675 TYR 0.017 0.003 TYR D 226 ARG 0.010 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 358 time to evaluate : 2.250 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6584 (mtpp) REVERT: A 144 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6906 (tpp-160) REVERT: A 317 VAL cc_start: 0.6759 (OUTLIER) cc_final: 0.6399 (p) REVERT: A 414 ARG cc_start: 0.7153 (ptt180) cc_final: 0.6806 (ptt180) REVERT: A 421 ARG cc_start: 0.7747 (mtm110) cc_final: 0.7476 (mtp-110) REVERT: A 431 ASP cc_start: 0.6515 (m-30) cc_final: 0.6199 (m-30) REVERT: A 433 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6755 (tp) REVERT: A 454 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7304 (mtmm) REVERT: A 562 ASP cc_start: 0.5715 (p0) cc_final: 0.5359 (p0) REVERT: A 623 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6287 (p90) REVERT: A 708 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6958 (tptp) REVERT: B 68 LYS cc_start: 0.7438 (mttt) cc_final: 0.7225 (mttm) REVERT: B 75 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6512 (mttp) REVERT: B 141 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6711 (mptt) REVERT: B 144 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6984 (tpp-160) REVERT: B 156 LYS cc_start: 0.7291 (mtmm) cc_final: 0.6856 (mtmt) REVERT: B 299 SER cc_start: 0.5021 (OUTLIER) cc_final: 0.4674 (t) REVERT: B 452 ASP cc_start: 0.6659 (m-30) cc_final: 0.6018 (t0) REVERT: B 522 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6621 (mptt) REVERT: B 581 ASN cc_start: 0.7163 (t0) cc_final: 0.6882 (t0) REVERT: B 623 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6236 (p90) REVERT: C 75 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6753 (mtpp) REVERT: C 79 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6622 (ttpt) REVERT: C 144 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6883 (tpp-160) REVERT: C 156 LYS cc_start: 0.7270 (mtmm) cc_final: 0.6805 (mtmt) REVERT: C 317 VAL cc_start: 0.6743 (OUTLIER) cc_final: 0.6393 (p) REVERT: C 571 LEU cc_start: 0.7143 (mt) cc_final: 0.6938 (mt) REVERT: C 575 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6347 (mm) REVERT: C 623 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6318 (p90) REVERT: C 708 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6983 (mmtt) REVERT: D 133 TRP cc_start: 0.5670 (m-10) cc_final: 0.5415 (m-10) REVERT: D 144 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6869 (tpp-160) REVERT: D 299 SER cc_start: 0.5372 (OUTLIER) cc_final: 0.5024 (t) REVERT: D 414 ARG cc_start: 0.7181 (ptt180) cc_final: 0.6766 (ptt180) REVERT: D 539 LYS cc_start: 0.6796 (tttp) cc_final: 0.6440 (mtpp) REVERT: D 623 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6267 (p90) REVERT: D 674 LYS cc_start: 0.7123 (tttp) cc_final: 0.6730 (tttm) REVERT: D 708 LYS cc_start: 0.7207 (mtmt) cc_final: 0.6806 (mmtt) outliers start: 140 outliers final: 92 residues processed: 463 average time/residue: 1.4886 time to fit residues: 769.1663 Evaluate side-chains 470 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 357 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 666 ARG Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 0.0970 chunk 217 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21368 Z= 0.222 Angle : 0.612 12.740 29068 Z= 0.313 Chirality : 0.043 0.150 3051 Planarity : 0.005 0.053 3825 Dihedral : 10.151 82.256 3030 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.08 % Allowed : 23.24 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.32 (0.16), residues: 2630 helix: 0.33 (0.15), residues: 1093 sheet: 0.35 (0.55), residues: 78 loop : -0.62 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 338 HIS 0.009 0.002 HIS D 49 PHE 0.015 0.002 PHE A 675 TYR 0.014 0.002 TYR A 226 ARG 0.007 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 361 time to evaluate : 2.370 Fit side-chains REVERT: A 144 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6849 (tpp-160) REVERT: A 163 PHE cc_start: 0.7859 (m-80) cc_final: 0.7615 (m-80) REVERT: A 317 VAL cc_start: 0.6740 (t) cc_final: 0.6353 (p) REVERT: A 414 ARG cc_start: 0.7218 (ptt180) cc_final: 0.6895 (ptt180) REVERT: A 421 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7384 (mtp-110) REVERT: A 433 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6599 (tp) REVERT: A 479 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6800 (mtp180) REVERT: A 562 ASP cc_start: 0.5658 (p0) cc_final: 0.5348 (p0) REVERT: A 623 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.6211 (p90) REVERT: A 708 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6908 (tptp) REVERT: B 75 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6620 (mttp) REVERT: B 112 ARG cc_start: 0.6466 (mtp180) cc_final: 0.6208 (mtm110) REVERT: B 141 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7123 (mppt) REVERT: B 144 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6974 (tpp-160) REVERT: B 156 LYS cc_start: 0.7321 (mtmm) cc_final: 0.6883 (mtmt) REVERT: B 299 SER cc_start: 0.4986 (OUTLIER) cc_final: 0.4700 (t) REVERT: B 452 ASP cc_start: 0.6638 (m-30) cc_final: 0.6086 (t0) REVERT: B 522 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6606 (mptt) REVERT: B 575 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6193 (mm) REVERT: B 581 ASN cc_start: 0.7009 (t0) cc_final: 0.6710 (t0) REVERT: B 583 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.5667 (ttt-90) REVERT: B 623 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6388 (p90) REVERT: B 674 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6945 (tttm) REVERT: C 75 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6711 (mtpp) REVERT: C 144 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6813 (tpp-160) REVERT: C 156 LYS cc_start: 0.7304 (mtmm) cc_final: 0.6836 (mtmt) REVERT: C 299 SER cc_start: 0.5759 (OUTLIER) cc_final: 0.5506 (t) REVERT: C 317 VAL cc_start: 0.6691 (t) cc_final: 0.6378 (p) REVERT: C 359 ILE cc_start: 0.5246 (OUTLIER) cc_final: 0.4831 (mp) REVERT: C 414 ARG cc_start: 0.7177 (ptt180) cc_final: 0.6833 (ptt180) REVERT: C 575 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6216 (mm) REVERT: C 623 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6096 (p90) REVERT: C 708 LYS cc_start: 0.7215 (mtmt) cc_final: 0.6903 (mmtt) REVERT: D 133 TRP cc_start: 0.5629 (m-10) cc_final: 0.5383 (m-10) REVERT: D 144 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6837 (tpp-160) REVERT: D 299 SER cc_start: 0.5035 (OUTLIER) cc_final: 0.4788 (t) REVERT: D 414 ARG cc_start: 0.7216 (ptt180) cc_final: 0.6851 (ptt180) REVERT: D 452 ASP cc_start: 0.6500 (m-30) cc_final: 0.5988 (t70) REVERT: D 479 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7072 (mtp180) REVERT: D 539 LYS cc_start: 0.6794 (tttp) cc_final: 0.6406 (mtpp) REVERT: D 623 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6042 (p90) REVERT: D 674 LYS cc_start: 0.7117 (tttp) cc_final: 0.6702 (tttm) REVERT: D 708 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6769 (mmtt) outliers start: 130 outliers final: 81 residues processed: 462 average time/residue: 1.4972 time to fit residues: 773.3839 Evaluate side-chains 458 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 353 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 149 optimal weight: 0.0370 chunk 62 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21368 Z= 0.264 Angle : 0.654 13.197 29068 Z= 0.336 Chirality : 0.044 0.159 3051 Planarity : 0.005 0.053 3825 Dihedral : 10.168 87.822 3013 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 7.06 % Allowed : 22.39 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.33 (0.16), residues: 2630 helix: 0.28 (0.15), residues: 1100 sheet: 0.42 (0.55), residues: 78 loop : -0.60 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 338 HIS 0.009 0.002 HIS C 49 PHE 0.014 0.002 PHE B 675 TYR 0.021 0.002 TYR A 226 ARG 0.009 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 353 time to evaluate : 2.492 Fit side-chains REVERT: A 144 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6809 (tpp-160) REVERT: A 317 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6398 (p) REVERT: A 414 ARG cc_start: 0.7272 (ptt180) cc_final: 0.6926 (ptt180) REVERT: A 421 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7382 (mtp-110) REVERT: A 433 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6725 (tp) REVERT: A 562 ASP cc_start: 0.5653 (p0) cc_final: 0.5357 (p0) REVERT: A 623 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6018 (p90) REVERT: A 708 LYS cc_start: 0.7232 (mtmt) cc_final: 0.6916 (tptp) REVERT: B 68 LYS cc_start: 0.7486 (mttt) cc_final: 0.7270 (mttm) REVERT: B 75 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6548 (mttp) REVERT: B 141 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7106 (mppt) REVERT: B 144 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6869 (tpp-160) REVERT: B 156 LYS cc_start: 0.7314 (mtmm) cc_final: 0.6897 (mtmt) REVERT: B 299 SER cc_start: 0.5201 (OUTLIER) cc_final: 0.4863 (t) REVERT: B 452 ASP cc_start: 0.6651 (m-30) cc_final: 0.6063 (t0) REVERT: B 522 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6582 (mptt) REVERT: B 575 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6188 (mm) REVERT: B 581 ASN cc_start: 0.7011 (t0) cc_final: 0.6647 (t0) REVERT: B 583 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.5813 (ttt-90) REVERT: B 623 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6153 (p90) REVERT: B 674 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6863 (tttm) REVERT: C 75 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6749 (mtpp) REVERT: C 144 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6828 (tpp-160) REVERT: C 156 LYS cc_start: 0.7314 (mtmm) cc_final: 0.6861 (mtmt) REVERT: C 299 SER cc_start: 0.5729 (OUTLIER) cc_final: 0.5463 (t) REVERT: C 359 ILE cc_start: 0.5251 (OUTLIER) cc_final: 0.4872 (mp) REVERT: C 414 ARG cc_start: 0.7196 (ptt180) cc_final: 0.6854 (ptt180) REVERT: C 575 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6165 (mm) REVERT: C 623 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6350 (p90) REVERT: C 708 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6926 (mmtt) REVERT: D 68 LYS cc_start: 0.7487 (mttt) cc_final: 0.7180 (mttm) REVERT: D 133 TRP cc_start: 0.5649 (m-10) cc_final: 0.5405 (m-10) REVERT: D 144 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6854 (tpp-160) REVERT: D 299 SER cc_start: 0.5257 (OUTLIER) cc_final: 0.4947 (t) REVERT: D 414 ARG cc_start: 0.7213 (ptt180) cc_final: 0.6836 (ptt180) REVERT: D 447 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: D 479 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7042 (mtp180) REVERT: D 522 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6836 (mptp) REVERT: D 539 LYS cc_start: 0.6799 (tttp) cc_final: 0.6419 (mtpp) REVERT: D 565 ASP cc_start: 0.6376 (t70) cc_final: 0.5971 (t0) REVERT: D 623 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.6021 (p90) REVERT: D 674 LYS cc_start: 0.7112 (tttp) cc_final: 0.6715 (tttm) outliers start: 151 outliers final: 95 residues processed: 469 average time/residue: 1.4304 time to fit residues: 751.1707 Evaluate side-chains 474 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 354 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 641 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21368 Z= 0.160 Angle : 0.545 10.827 29068 Z= 0.275 Chirality : 0.041 0.153 3051 Planarity : 0.004 0.052 3825 Dihedral : 9.336 75.554 3013 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.66 % Allowed : 24.03 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.06 (0.16), residues: 2630 helix: 0.76 (0.15), residues: 1107 sheet: 0.36 (0.53), residues: 78 loop : -0.50 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 338 HIS 0.005 0.001 HIS D 49 PHE 0.012 0.001 PHE A 386 TYR 0.014 0.001 TYR A 226 ARG 0.005 0.000 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 370 time to evaluate : 2.320 Fit side-chains REVERT: A 144 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6881 (tpp-160) REVERT: A 310 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.5773 (mm) REVERT: A 317 VAL cc_start: 0.6695 (t) cc_final: 0.6311 (p) REVERT: A 414 ARG cc_start: 0.7166 (ptt180) cc_final: 0.6831 (ptt180) REVERT: A 421 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7384 (mtp-110) REVERT: A 431 ASP cc_start: 0.6466 (m-30) cc_final: 0.6159 (m-30) REVERT: A 433 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6513 (tp) REVERT: A 479 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7017 (mtp180) REVERT: A 562 ASP cc_start: 0.5628 (p0) cc_final: 0.5376 (p0) REVERT: A 598 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.6873 (tmtp) REVERT: A 623 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6014 (p90) REVERT: A 674 LYS cc_start: 0.7127 (tttm) cc_final: 0.6872 (tmtm) REVERT: A 708 LYS cc_start: 0.7156 (mtmt) cc_final: 0.6756 (mmtt) REVERT: B 68 LYS cc_start: 0.7318 (mttt) cc_final: 0.7090 (mttm) REVERT: B 112 ARG cc_start: 0.6449 (mtp180) cc_final: 0.6212 (mtm110) REVERT: B 144 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6772 (tpp-160) REVERT: B 156 LYS cc_start: 0.7286 (mtmm) cc_final: 0.6881 (mtmt) REVERT: B 299 SER cc_start: 0.5164 (OUTLIER) cc_final: 0.4855 (t) REVERT: B 414 ARG cc_start: 0.7021 (ptt180) cc_final: 0.6597 (ptt180) REVERT: B 448 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6753 (tp40) REVERT: B 452 ASP cc_start: 0.6503 (m-30) cc_final: 0.6044 (t70) REVERT: B 479 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6888 (mtp180) REVERT: B 522 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6610 (mptt) REVERT: B 575 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6098 (mm) REVERT: B 581 ASN cc_start: 0.6948 (t0) cc_final: 0.6416 (t0) REVERT: B 583 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6002 (tpt-90) REVERT: B 598 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.6660 (tmtp) REVERT: B 622 ASN cc_start: 0.7213 (m-40) cc_final: 0.7005 (m-40) REVERT: B 623 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.6193 (p90) REVERT: B 674 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6879 (tttm) REVERT: C 144 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6900 (tpp-160) REVERT: C 156 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6819 (mtmt) REVERT: C 299 SER cc_start: 0.5907 (OUTLIER) cc_final: 0.5612 (t) REVERT: C 414 ARG cc_start: 0.7001 (ptt180) cc_final: 0.6656 (ptt180) REVERT: C 448 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6556 (tp40) REVERT: C 479 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6891 (mtp180) REVERT: C 562 ASP cc_start: 0.5546 (p0) cc_final: 0.5126 (p0) REVERT: C 598 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.6866 (tmtp) REVERT: C 708 LYS cc_start: 0.7162 (mtmt) cc_final: 0.6834 (mmtt) REVERT: D 133 TRP cc_start: 0.5640 (m-10) cc_final: 0.5361 (m-10) REVERT: D 144 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6895 (tpp-160) REVERT: D 414 ARG cc_start: 0.7096 (ptt180) cc_final: 0.6774 (ptt180) REVERT: D 447 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6702 (tt0) REVERT: D 448 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6861 (tp40) REVERT: D 452 ASP cc_start: 0.6404 (m-30) cc_final: 0.6005 (t70) REVERT: D 479 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7120 (mtp180) REVERT: D 539 LYS cc_start: 0.6756 (tttp) cc_final: 0.6284 (mtpp) REVERT: D 580 ARG cc_start: 0.7667 (ptt180) cc_final: 0.7345 (ptm160) REVERT: D 598 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.6875 (tmtp) REVERT: D 623 PHE cc_start: 0.6471 (OUTLIER) cc_final: 0.5942 (p90) REVERT: D 674 LYS cc_start: 0.7181 (tttp) cc_final: 0.6752 (tttm) outliers start: 121 outliers final: 58 residues processed: 464 average time/residue: 1.4701 time to fit residues: 763.1753 Evaluate side-chains 453 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 367 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 637 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 0.0020 chunk 161 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21368 Z= 0.284 Angle : 0.668 12.830 29068 Z= 0.343 Chirality : 0.045 0.182 3051 Planarity : 0.005 0.052 3825 Dihedral : 9.741 84.407 3001 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.70 % Allowed : 24.26 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.17 (0.16), residues: 2630 helix: 0.47 (0.15), residues: 1097 sheet: 0.45 (0.54), residues: 78 loop : -0.54 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 93 HIS 0.008 0.002 HIS C 49 PHE 0.020 0.003 PHE B 455 TYR 0.021 0.003 TYR B 582 ARG 0.009 0.001 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 354 time to evaluate : 2.170 Fit side-chains REVERT: A 75 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6675 (mtpp) REVERT: A 144 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6838 (tpp-160) REVERT: A 317 VAL cc_start: 0.6723 (OUTLIER) cc_final: 0.6375 (p) REVERT: A 414 ARG cc_start: 0.7225 (ptt180) cc_final: 0.6850 (ptt180) REVERT: A 421 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7374 (mtp-110) REVERT: A 433 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6730 (tp) REVERT: A 479 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6973 (mtp180) REVERT: A 562 ASP cc_start: 0.5680 (p0) cc_final: 0.5400 (p0) REVERT: A 623 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6201 (p90) REVERT: A 708 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6861 (mmtt) REVERT: B 68 LYS cc_start: 0.7466 (mttt) cc_final: 0.7217 (mttm) REVERT: B 75 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6634 (mtpp) REVERT: B 141 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7136 (mppt) REVERT: B 144 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6957 (tpp-160) REVERT: B 156 LYS cc_start: 0.7296 (mtmm) cc_final: 0.6900 (mtmt) REVERT: B 299 SER cc_start: 0.5173 (OUTLIER) cc_final: 0.4834 (t) REVERT: B 414 ARG cc_start: 0.7049 (ptt180) cc_final: 0.6662 (ptt180) REVERT: B 452 ASP cc_start: 0.6647 (m-30) cc_final: 0.6082 (t0) REVERT: B 522 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6572 (mptt) REVERT: B 575 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6233 (mm) REVERT: B 581 ASN cc_start: 0.7007 (t0) cc_final: 0.6641 (t0) REVERT: B 583 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.5800 (ttt-90) REVERT: B 623 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6212 (p90) REVERT: C 144 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6889 (tpp-160) REVERT: C 156 LYS cc_start: 0.7331 (mtmm) cc_final: 0.6842 (mtmt) REVERT: C 299 SER cc_start: 0.5934 (OUTLIER) cc_final: 0.5616 (t) REVERT: C 317 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6303 (p) REVERT: C 414 ARG cc_start: 0.7022 (ptt180) cc_final: 0.6681 (ptt180) REVERT: C 575 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6124 (mm) REVERT: C 623 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6199 (p90) REVERT: C 708 LYS cc_start: 0.7261 (mtmt) cc_final: 0.6949 (mmtt) REVERT: D 133 TRP cc_start: 0.5674 (m-10) cc_final: 0.5398 (m-10) REVERT: D 144 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6861 (tpp-160) REVERT: D 414 ARG cc_start: 0.7142 (ptt180) cc_final: 0.6736 (ptt180) REVERT: D 447 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6717 (tt0) REVERT: D 479 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7085 (mtp180) REVERT: D 539 LYS cc_start: 0.6768 (tttp) cc_final: 0.6393 (mtpp) REVERT: D 623 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5950 (p90) REVERT: D 674 LYS cc_start: 0.7143 (tttp) cc_final: 0.6739 (tttm) outliers start: 122 outliers final: 79 residues processed: 448 average time/residue: 1.5123 time to fit residues: 755.3905 Evaluate side-chains 458 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 355 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 214 optimal weight: 0.0670 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21368 Z= 0.142 Angle : 0.523 9.803 29068 Z= 0.262 Chirality : 0.040 0.161 3051 Planarity : 0.004 0.052 3825 Dihedral : 8.629 67.149 3001 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.69 % Allowed : 26.41 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.29 (0.16), residues: 2630 helix: 1.01 (0.15), residues: 1106 sheet: 0.39 (0.52), residues: 78 loop : -0.42 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 338 HIS 0.003 0.001 HIS C 49 PHE 0.012 0.001 PHE A 675 TYR 0.014 0.001 TYR A 226 ARG 0.007 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 369 time to evaluate : 2.485 Fit side-chains REVERT: A 144 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6749 (tpp-160) REVERT: A 317 VAL cc_start: 0.6637 (t) cc_final: 0.6250 (p) REVERT: A 414 ARG cc_start: 0.7043 (ptt180) cc_final: 0.6726 (ptt180) REVERT: A 421 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7379 (mtp-110) REVERT: A 431 ASP cc_start: 0.6475 (m-30) cc_final: 0.6169 (m-30) REVERT: A 479 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6976 (mtp180) REVERT: A 562 ASP cc_start: 0.5667 (p0) cc_final: 0.5390 (p0) REVERT: A 592 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: A 598 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.6805 (tmtp) REVERT: A 623 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.5992 (p90) REVERT: A 627 LYS cc_start: 0.7478 (mtpt) cc_final: 0.7254 (mtpp) REVERT: B 112 ARG cc_start: 0.6474 (mtp180) cc_final: 0.6168 (mtm-85) REVERT: B 141 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6896 (mptm) REVERT: B 144 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6772 (tpp-160) REVERT: B 156 LYS cc_start: 0.7320 (mtmm) cc_final: 0.6914 (mtmt) REVERT: B 299 SER cc_start: 0.5242 (OUTLIER) cc_final: 0.4944 (t) REVERT: B 373 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6768 (mmt) REVERT: B 414 ARG cc_start: 0.6922 (ptt180) cc_final: 0.6570 (ptt180) REVERT: B 452 ASP cc_start: 0.6455 (m-30) cc_final: 0.6034 (t70) REVERT: B 479 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6953 (mtp180) REVERT: B 580 ARG cc_start: 0.7535 (ptt180) cc_final: 0.7273 (ptm160) REVERT: B 581 ASN cc_start: 0.6761 (t0) cc_final: 0.6282 (t0) REVERT: B 583 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6152 (tpt-90) REVERT: B 592 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: B 598 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.6735 (tmtp) REVERT: B 623 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.6182 (p90) REVERT: B 674 LYS cc_start: 0.7171 (tttp) cc_final: 0.6870 (tttm) REVERT: C 144 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6853 (tpp-160) REVERT: C 156 LYS cc_start: 0.7354 (mtmm) cc_final: 0.6998 (mtmt) REVERT: C 414 ARG cc_start: 0.6816 (ptt180) cc_final: 0.6535 (ptt180) REVERT: C 479 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7001 (mtp180) REVERT: C 562 ASP cc_start: 0.5550 (p0) cc_final: 0.5156 (p0) REVERT: C 592 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: C 598 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.6846 (tmtp) REVERT: C 708 LYS cc_start: 0.7178 (mtmt) cc_final: 0.6825 (mmtt) REVERT: D 133 TRP cc_start: 0.5674 (m-10) cc_final: 0.5424 (m-10) REVERT: D 144 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6857 (tpp-160) REVERT: D 414 ARG cc_start: 0.6966 (ptt180) cc_final: 0.6620 (ptt180) REVERT: D 447 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: D 448 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6776 (tp40) REVERT: D 452 ASP cc_start: 0.6375 (m-30) cc_final: 0.5969 (t70) REVERT: D 539 LYS cc_start: 0.6721 (tttp) cc_final: 0.6333 (mtpp) REVERT: D 580 ARG cc_start: 0.7672 (ptt180) cc_final: 0.7372 (ptm160) REVERT: D 598 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.6740 (tmtp) REVERT: D 623 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5611 (p90) REVERT: D 674 LYS cc_start: 0.7187 (tttp) cc_final: 0.6751 (tttm) outliers start: 79 outliers final: 43 residues processed: 432 average time/residue: 1.5190 time to fit residues: 733.5512 Evaluate side-chains 427 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 360 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 637 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 5.9990 chunk 153 optimal weight: 0.0060 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21368 Z= 0.159 Angle : 0.541 9.627 29068 Z= 0.272 Chirality : 0.040 0.162 3051 Planarity : 0.005 0.052 3825 Dihedral : 8.277 70.158 2987 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.69 % Allowed : 26.74 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.35 (0.16), residues: 2630 helix: 1.07 (0.15), residues: 1107 sheet: 0.45 (0.52), residues: 78 loop : -0.40 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 93 HIS 0.005 0.001 HIS B 49 PHE 0.024 0.001 PHE C 455 TYR 0.015 0.001 TYR D 226 ARG 0.008 0.000 ARG C 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 355 time to evaluate : 2.833 Fit side-chains REVERT: A 144 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6840 (tpp-160) REVERT: A 317 VAL cc_start: 0.6657 (t) cc_final: 0.6261 (p) REVERT: A 414 ARG cc_start: 0.7133 (ptt180) cc_final: 0.6819 (ptt180) REVERT: A 421 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7398 (mtp-110) REVERT: A 431 ASP cc_start: 0.6433 (m-30) cc_final: 0.6140 (m-30) REVERT: A 479 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6957 (mtt180) REVERT: A 562 ASP cc_start: 0.5675 (p0) cc_final: 0.5393 (p0) REVERT: A 598 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.6739 (tmtp) REVERT: A 627 LYS cc_start: 0.7411 (mtpt) cc_final: 0.7156 (mtpp) REVERT: A 708 LYS cc_start: 0.7172 (mtmt) cc_final: 0.6897 (mptt) REVERT: B 141 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6889 (mptm) REVERT: B 144 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6884 (tpp-160) REVERT: B 156 LYS cc_start: 0.7335 (mtmm) cc_final: 0.7016 (mtmt) REVERT: B 299 SER cc_start: 0.5246 (OUTLIER) cc_final: 0.4923 (t) REVERT: B 414 ARG cc_start: 0.6936 (ptt180) cc_final: 0.6549 (ptt180) REVERT: B 452 ASP cc_start: 0.6421 (m-30) cc_final: 0.5990 (t70) REVERT: B 479 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7074 (mtp180) REVERT: B 581 ASN cc_start: 0.6504 (t0) cc_final: 0.6298 (t0) REVERT: B 583 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6173 (tpt-90) REVERT: B 592 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5871 (mp0) REVERT: B 667 ASP cc_start: 0.5019 (OUTLIER) cc_final: 0.4735 (t70) REVERT: C 144 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6883 (tpp-160) REVERT: C 156 LYS cc_start: 0.7506 (mtmm) cc_final: 0.7035 (mtmt) REVERT: C 414 ARG cc_start: 0.6953 (ptt180) cc_final: 0.6674 (ptt180) REVERT: C 479 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6953 (mtp180) REVERT: C 562 ASP cc_start: 0.5608 (p0) cc_final: 0.5186 (p0) REVERT: C 598 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.6789 (tmtp) REVERT: C 708 LYS cc_start: 0.7183 (mtmt) cc_final: 0.6826 (mmtt) REVERT: D 133 TRP cc_start: 0.5692 (m-10) cc_final: 0.5429 (m-10) REVERT: D 144 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6877 (tpp-160) REVERT: D 414 ARG cc_start: 0.7001 (ptt180) cc_final: 0.6704 (ptt180) REVERT: D 447 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: D 448 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6891 (tp40) REVERT: D 452 ASP cc_start: 0.6385 (m-30) cc_final: 0.5990 (t70) REVERT: D 539 LYS cc_start: 0.6721 (tttp) cc_final: 0.6335 (mtpp) REVERT: D 598 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.6753 (tmtp) REVERT: D 623 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.5674 (p90) REVERT: D 674 LYS cc_start: 0.7191 (tttp) cc_final: 0.6752 (tttm) outliers start: 79 outliers final: 51 residues processed: 419 average time/residue: 1.5584 time to fit residues: 730.6215 Evaluate side-chains 419 residues out of total 2139 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 350 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 583 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 637 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 193 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 215 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.191901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.173775 restraints weight = 180732.584| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 5.45 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.174 21368 Z= 0.196 Angle : 0.707 59.200 29068 Z= 0.400 Chirality : 0.044 1.023 3051 Planarity : 0.005 0.059 3825 Dihedral : 8.222 70.217 2982 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 3.60 % Allowed : 27.07 % Favored : 69.33 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.34 (0.16), residues: 2630 helix: 1.05 (0.15), residues: 1107 sheet: 0.45 (0.52), residues: 78 loop : -0.39 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 93 HIS 0.005 0.001 HIS B 49 PHE 0.016 0.002 PHE A 675 TYR 0.017 0.002 TYR B 226 ARG 0.009 0.000 ARG B 185 =============================================================================== Job complete usr+sys time: 9978.49 seconds wall clock time: 176 minutes 21.58 seconds (10581.58 seconds total)