Starting phenix.real_space_refine on Mon Mar 11 08:54:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/03_2024/5wq8_6676_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/03_2024/5wq8_6676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/03_2024/5wq8_6676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/03_2024/5wq8_6676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/03_2024/5wq8_6676_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/03_2024/5wq8_6676_neut.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 35235 2.51 5 N 9885 2.21 5 O 11145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A ARG 598": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 521": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ARG 521": "NH1" <-> "NH2" Residue "E ARG 598": "NH1" <-> "NH2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 598": "NH1" <-> "NH2" Residue "F ARG 604": "NH1" <-> "NH2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "G ARG 521": "NH1" <-> "NH2" Residue "G ARG 598": "NH1" <-> "NH2" Residue "G ARG 604": "NH1" <-> "NH2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H ARG 521": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 604": "NH1" <-> "NH2" Residue "I GLU 253": "OE1" <-> "OE2" Residue "I ARG 521": "NH1" <-> "NH2" Residue "I ARG 598": "NH1" <-> "NH2" Residue "I ARG 604": "NH1" <-> "NH2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "J ARG 521": "NH1" <-> "NH2" Residue "J ARG 598": "NH1" <-> "NH2" Residue "J ARG 604": "NH1" <-> "NH2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K ARG 521": "NH1" <-> "NH2" Residue "K ARG 598": "NH1" <-> "NH2" Residue "K ARG 604": "NH1" <-> "NH2" Residue "L GLU 253": "OE1" <-> "OE2" Residue "L ARG 521": "NH1" <-> "NH2" Residue "L ARG 598": "NH1" <-> "NH2" Residue "L ARG 604": "NH1" <-> "NH2" Residue "M GLU 253": "OE1" <-> "OE2" Residue "M ARG 521": "NH1" <-> "NH2" Residue "M ARG 598": "NH1" <-> "NH2" Residue "M ARG 604": "NH1" <-> "NH2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N ARG 521": "NH1" <-> "NH2" Residue "N ARG 598": "NH1" <-> "NH2" Residue "N ARG 604": "NH1" <-> "NH2" Residue "O GLU 253": "OE1" <-> "OE2" Residue "O ARG 521": "NH1" <-> "NH2" Residue "O ARG 598": "NH1" <-> "NH2" Residue "O ARG 604": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 56460 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "B" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "C" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "D" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "E" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "F" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "G" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "H" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "I" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "J" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "K" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "L" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "M" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "N" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Chain: "O" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3764 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 481} Chain breaks: 4 Time building chain proxies: 21.22, per 1000 atoms: 0.38 Number of scatterers: 56460 At special positions: 0 Unit cell: (175.56, 174.24, 203.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 11145 8.00 N 9885 7.00 C 35235 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=0, symmetry=0 Time building additional restraints: 16.94 Conformation dependent library (CDL) restraints added in 8.6 seconds 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13800 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 62 sheets defined 33.1% alpha, 52.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL A 623 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU B 308 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL B 623 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL C 623 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 Processing helix chain 'D' and resid 397 through 405 Processing helix chain 'D' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA D 592 " --> pdb=" O ASP D 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL D 623 " --> pdb=" O ASP D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN D 645 " --> pdb=" O ALA D 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 161 Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU E 308 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 397 through 405 Processing helix chain 'E' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 removed outlier: 4.088A pdb=" N PHE E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA E 592 " --> pdb=" O ASP E 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE E 603 " --> pdb=" O LYS E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL E 623 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN E 645 " --> pdb=" O ALA E 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 161 Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU F 308 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 397 through 405 Processing helix chain 'F' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE F 558 " --> pdb=" O LEU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA F 592 " --> pdb=" O ASP F 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 603 " --> pdb=" O LYS F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL F 623 " --> pdb=" O ASP F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 646 removed outlier: 3.639A pdb=" N GLN F 645 " --> pdb=" O ALA F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 114 Processing helix chain 'G' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 161 Processing helix chain 'G' and resid 176 through 186 Processing helix chain 'G' and resid 218 through 232 removed outlier: 3.792A pdb=" N LEU G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL G 262 " --> pdb=" O VAL G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU G 308 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 Processing helix chain 'G' and resid 397 through 405 Processing helix chain 'G' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 561 through 566 removed outlier: 4.088A pdb=" N PHE G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA G 592 " --> pdb=" O ASP G 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE G 603 " --> pdb=" O LYS G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL G 623 " --> pdb=" O ASP G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN G 645 " --> pdb=" O ALA G 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 114 Processing helix chain 'H' and resid 115 through 126 removed outlier: 3.887A pdb=" N ALA H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 161 Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU H 308 " --> pdb=" O ASN H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 370 Processing helix chain 'H' and resid 397 through 405 Processing helix chain 'H' and resid 553 through 558 removed outlier: 4.072A pdb=" N ILE H 558 " --> pdb=" O LEU H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE H 565 " --> pdb=" O LEU H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA H 592 " --> pdb=" O ASP H 588 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE H 603 " --> pdb=" O LYS H 599 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL H 623 " --> pdb=" O ASP H 620 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN H 645 " --> pdb=" O ALA H 641 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 Processing helix chain 'I' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 161 Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY I 261 " --> pdb=" O GLU I 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL I 262 " --> pdb=" O VAL I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU I 308 " --> pdb=" O ASN I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 370 Processing helix chain 'I' and resid 397 through 405 Processing helix chain 'I' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE I 558 " --> pdb=" O LEU I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA I 592 " --> pdb=" O ASP I 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE I 603 " --> pdb=" O LYS I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL I 623 " --> pdb=" O ASP I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 636 through 646 removed outlier: 3.637A pdb=" N GLN I 645 " --> pdb=" O ALA I 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 Processing helix chain 'J' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 161 Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY J 261 " --> pdb=" O GLU J 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL J 262 " --> pdb=" O VAL J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU J 308 " --> pdb=" O ASN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 370 Processing helix chain 'J' and resid 397 through 405 Processing helix chain 'J' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE J 558 " --> pdb=" O LEU J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE J 565 " --> pdb=" O LEU J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA J 592 " --> pdb=" O ASP J 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE J 603 " --> pdb=" O LYS J 599 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL J 623 " --> pdb=" O ASP J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN J 645 " --> pdb=" O ALA J 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 Processing helix chain 'K' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 161 Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL K 262 " --> pdb=" O VAL K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU K 308 " --> pdb=" O ASN K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 370 Processing helix chain 'K' and resid 397 through 405 Processing helix chain 'K' and resid 553 through 558 removed outlier: 4.072A pdb=" N ILE K 558 " --> pdb=" O LEU K 554 " (cutoff:3.500A) Processing helix chain 'K' and resid 561 through 566 removed outlier: 4.088A pdb=" N PHE K 565 " --> pdb=" O LEU K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA K 592 " --> pdb=" O ASP K 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE K 603 " --> pdb=" O LYS K 599 " (cutoff:3.500A) Processing helix chain 'K' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL K 623 " --> pdb=" O ASP K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN K 645 " --> pdb=" O ALA K 641 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 114 Processing helix chain 'L' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 161 Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY L 261 " --> pdb=" O GLU L 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL L 262 " --> pdb=" O VAL L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU L 308 " --> pdb=" O ASN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 370 Processing helix chain 'L' and resid 397 through 405 Processing helix chain 'L' and resid 553 through 558 removed outlier: 4.072A pdb=" N ILE L 558 " --> pdb=" O LEU L 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE L 565 " --> pdb=" O LEU L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA L 592 " --> pdb=" O ASP L 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE L 603 " --> pdb=" O LYS L 599 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL L 623 " --> pdb=" O ASP L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN L 645 " --> pdb=" O ALA L 641 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 Processing helix chain 'M' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA M 126 " --> pdb=" O LEU M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 161 Processing helix chain 'M' and resid 176 through 186 Processing helix chain 'M' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU M 232 " --> pdb=" O LEU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL M 262 " --> pdb=" O VAL M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU M 308 " --> pdb=" O ASN M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 370 Processing helix chain 'M' and resid 397 through 405 Processing helix chain 'M' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE M 558 " --> pdb=" O LEU M 554 " (cutoff:3.500A) Processing helix chain 'M' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE M 565 " --> pdb=" O LEU M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA M 592 " --> pdb=" O ASP M 588 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE M 603 " --> pdb=" O LYS M 599 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 623 removed outlier: 3.843A pdb=" N VAL M 623 " --> pdb=" O ASP M 620 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN M 645 " --> pdb=" O ALA M 641 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 114 Processing helix chain 'N' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 161 Processing helix chain 'N' and resid 176 through 186 Processing helix chain 'N' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL N 262 " --> pdb=" O VAL N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU N 308 " --> pdb=" O ASN N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 370 Processing helix chain 'N' and resid 397 through 405 Processing helix chain 'N' and resid 553 through 558 removed outlier: 4.071A pdb=" N ILE N 558 " --> pdb=" O LEU N 554 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 566 removed outlier: 4.090A pdb=" N PHE N 565 " --> pdb=" O LEU N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA N 592 " --> pdb=" O ASP N 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE N 603 " --> pdb=" O LYS N 599 " (cutoff:3.500A) Processing helix chain 'N' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL N 623 " --> pdb=" O ASP N 620 " (cutoff:3.500A) Processing helix chain 'N' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN N 645 " --> pdb=" O ALA N 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 114 Processing helix chain 'O' and resid 115 through 126 removed outlier: 3.888A pdb=" N ALA O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 161 Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 218 through 232 removed outlier: 3.791A pdb=" N LEU O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 264 removed outlier: 4.529A pdb=" N GLY O 261 " --> pdb=" O GLU O 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL O 262 " --> pdb=" O VAL O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 314 removed outlier: 3.523A pdb=" N GLU O 308 " --> pdb=" O ASN O 304 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 370 Processing helix chain 'O' and resid 397 through 405 Processing helix chain 'O' and resid 553 through 558 removed outlier: 4.072A pdb=" N ILE O 558 " --> pdb=" O LEU O 554 " (cutoff:3.500A) Processing helix chain 'O' and resid 561 through 566 removed outlier: 4.089A pdb=" N PHE O 565 " --> pdb=" O LEU O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 588 through 613 removed outlier: 3.665A pdb=" N ALA O 592 " --> pdb=" O ASP O 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE O 603 " --> pdb=" O LYS O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 623 removed outlier: 3.844A pdb=" N VAL O 623 " --> pdb=" O ASP O 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 646 removed outlier: 3.638A pdb=" N GLN O 645 " --> pdb=" O ALA O 641 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 135 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE A 581 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL A 536 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU A 535 " --> pdb=" O MET B 443 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N MET B 443 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 537 " --> pdb=" O THR B 441 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 419 through 443 current: chain 'B' and resid 567 through 582 removed outlier: 6.595A pdb=" N ILE B 581 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL B 536 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU B 535 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET C 443 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 537 " --> pdb=" O THR C 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 581 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL C 536 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU C 535 " --> pdb=" O MET D 443 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N MET D 443 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C 537 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 581 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL E 536 " --> pdb=" O ILE E 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU E 535 " --> pdb=" O MET F 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET F 443 " --> pdb=" O LEU E 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU E 537 " --> pdb=" O THR F 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE F 581 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL F 536 " --> pdb=" O ILE F 581 " (cutoff:3.500A) removed outlier: 15.795A pdb=" N LEU F 535 " --> pdb=" O MET G 443 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N MET G 443 " --> pdb=" O LEU F 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU F 537 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE G 581 " --> pdb=" O VAL G 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL G 536 " --> pdb=" O ILE G 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU G 535 " --> pdb=" O MET H 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET H 443 " --> pdb=" O LEU G 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU G 537 " --> pdb=" O THR H 441 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE H 581 " --> pdb=" O VAL H 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL H 536 " --> pdb=" O ILE H 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU H 535 " --> pdb=" O MET I 443 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N MET I 443 " --> pdb=" O LEU H 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU H 537 " --> pdb=" O THR I 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 581 " --> pdb=" O VAL I 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL I 536 " --> pdb=" O ILE I 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU I 535 " --> pdb=" O MET J 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET J 443 " --> pdb=" O LEU I 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU I 537 " --> pdb=" O THR J 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE J 581 " --> pdb=" O VAL J 536 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL J 536 " --> pdb=" O ILE J 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU J 535 " --> pdb=" O MET K 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET K 443 " --> pdb=" O LEU J 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU J 537 " --> pdb=" O THR K 441 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE K 581 " --> pdb=" O VAL K 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL K 536 " --> pdb=" O ILE K 581 " (cutoff:3.500A) removed outlier: 15.793A pdb=" N LEU K 535 " --> pdb=" O MET L 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET L 443 " --> pdb=" O LEU K 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU K 537 " --> pdb=" O THR L 441 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE L 581 " --> pdb=" O VAL L 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL L 536 " --> pdb=" O ILE L 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU L 535 " --> pdb=" O MET M 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET M 443 " --> pdb=" O LEU L 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU L 537 " --> pdb=" O THR M 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 585 through 586 Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AA7, first strand: chain 'D' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE D 581 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL D 536 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU D 535 " --> pdb=" O MET E 443 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N MET E 443 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 537 " --> pdb=" O THR E 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 585 through 586 Processing sheet with id=AA9, first strand: chain 'F' and resid 585 through 586 Processing sheet with id=AB1, first strand: chain 'G' and resid 585 through 586 Processing sheet with id=AB2, first strand: chain 'H' and resid 585 through 586 Processing sheet with id=AB3, first strand: chain 'I' and resid 585 through 586 Processing sheet with id=AB4, first strand: chain 'J' and resid 585 through 586 Processing sheet with id=AB5, first strand: chain 'K' and resid 585 through 586 Processing sheet with id=AB6, first strand: chain 'L' and resid 585 through 586 Processing sheet with id=AB7, first strand: chain 'M' and resid 585 through 586 removed outlier: 6.595A pdb=" N ILE M 581 " --> pdb=" O VAL M 536 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL M 536 " --> pdb=" O ILE M 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU M 535 " --> pdb=" O MET N 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET N 443 " --> pdb=" O LEU M 535 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU M 537 " --> pdb=" O THR N 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 585 through 586 removed outlier: 6.596A pdb=" N ILE N 581 " --> pdb=" O VAL N 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL N 536 " --> pdb=" O ILE N 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU N 535 " --> pdb=" O MET O 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET O 443 " --> pdb=" O LEU N 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU N 537 " --> pdb=" O THR O 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 585 through 586 removed outlier: 6.596A pdb=" N ILE O 581 " --> pdb=" O VAL O 536 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL O 536 " --> pdb=" O ILE O 581 " (cutoff:3.500A) removed outlier: 15.794A pdb=" N LEU O 535 " --> pdb=" O MET A 443 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N MET A 443 " --> pdb=" O LEU O 535 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU O 537 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 372 through 377 removed outlier: 3.966A pdb=" N THR O 375 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR N 375 " --> pdb=" O THR O 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR M 375 " --> pdb=" O THR N 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR L 375 " --> pdb=" O THR M 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR K 375 " --> pdb=" O THR L 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR J 375 " --> pdb=" O THR K 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR I 375 " --> pdb=" O THR J 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR H 375 " --> pdb=" O THR I 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR G 375 " --> pdb=" O THR H 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR F 375 " --> pdb=" O THR G 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR E 375 " --> pdb=" O THR F 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR D 375 " --> pdb=" O THR E 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 375 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 375 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 375 " --> pdb=" O THR B 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 448 through 458 removed outlier: 12.572A pdb=" N GLU A 479 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL A 507 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 481 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 499 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU B 479 " --> pdb=" O VAL B 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL B 507 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 481 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 499 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU C 479 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL C 507 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY C 481 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C 499 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU D 479 " --> pdb=" O VAL D 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL D 507 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY D 481 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 499 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU E 479 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL E 507 " --> pdb=" O GLU E 479 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY E 481 " --> pdb=" O SER E 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN E 499 " --> pdb=" O VAL E 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU F 479 " --> pdb=" O VAL F 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL F 507 " --> pdb=" O GLU F 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY F 481 " --> pdb=" O SER F 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 499 " --> pdb=" O VAL F 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU G 479 " --> pdb=" O VAL G 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL G 507 " --> pdb=" O GLU G 479 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY G 481 " --> pdb=" O SER G 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 499 " --> pdb=" O VAL G 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU H 479 " --> pdb=" O VAL H 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL H 507 " --> pdb=" O GLU H 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY H 481 " --> pdb=" O SER H 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN H 499 " --> pdb=" O VAL H 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU I 479 " --> pdb=" O VAL I 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL I 507 " --> pdb=" O GLU I 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY I 481 " --> pdb=" O SER I 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN I 499 " --> pdb=" O VAL I 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU J 479 " --> pdb=" O VAL J 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL J 507 " --> pdb=" O GLU J 479 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY J 481 " --> pdb=" O SER J 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN J 499 " --> pdb=" O VAL J 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU K 479 " --> pdb=" O VAL K 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL K 507 " --> pdb=" O GLU K 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY K 481 " --> pdb=" O SER K 505 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN K 499 " --> pdb=" O VAL K 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU L 479 " --> pdb=" O VAL L 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL L 507 " --> pdb=" O GLU L 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY L 481 " --> pdb=" O SER L 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN L 499 " --> pdb=" O VAL L 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU M 479 " --> pdb=" O VAL M 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL M 507 " --> pdb=" O GLU M 479 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY M 481 " --> pdb=" O SER M 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN M 499 " --> pdb=" O VAL M 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU N 479 " --> pdb=" O VAL N 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL N 507 " --> pdb=" O GLU N 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY N 481 " --> pdb=" O SER N 505 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN N 499 " --> pdb=" O VAL N 487 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N GLU O 479 " --> pdb=" O VAL O 507 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL O 507 " --> pdb=" O GLU O 479 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY O 481 " --> pdb=" O SER O 505 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN O 499 " --> pdb=" O VAL O 487 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 135 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 166 through 171 Processing sheet with id=AC5, first strand: chain 'B' and resid 242 through 246 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.672A pdb=" N ILE C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP C 135 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AC8, first strand: chain 'C' and resid 242 through 246 Processing sheet with id=AC9, first strand: chain 'D' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 135 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 166 through 171 Processing sheet with id=AD2, first strand: chain 'D' and resid 242 through 246 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP E 135 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 166 through 171 Processing sheet with id=AD5, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AD6, first strand: chain 'F' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP F 135 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 166 through 171 Processing sheet with id=AD8, first strand: chain 'F' and resid 242 through 246 Processing sheet with id=AD9, first strand: chain 'G' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP G 135 " --> pdb=" O ILE G 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 166 through 171 Processing sheet with id=AE2, first strand: chain 'G' and resid 242 through 246 Processing sheet with id=AE3, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE H 139 " --> pdb=" O ASP H 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP H 135 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 166 through 171 Processing sheet with id=AE5, first strand: chain 'H' and resid 242 through 246 Processing sheet with id=AE6, first strand: chain 'I' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE I 139 " --> pdb=" O ASP I 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP I 135 " --> pdb=" O ILE I 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 166 through 171 Processing sheet with id=AE8, first strand: chain 'I' and resid 242 through 246 Processing sheet with id=AE9, first strand: chain 'J' and resid 100 through 104 removed outlier: 3.672A pdb=" N ILE J 139 " --> pdb=" O ASP J 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP J 135 " --> pdb=" O ILE J 139 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 166 through 171 Processing sheet with id=AF2, first strand: chain 'J' and resid 242 through 246 Processing sheet with id=AF3, first strand: chain 'K' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE K 139 " --> pdb=" O ASP K 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP K 135 " --> pdb=" O ILE K 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 166 through 171 Processing sheet with id=AF5, first strand: chain 'K' and resid 242 through 246 Processing sheet with id=AF6, first strand: chain 'L' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE L 139 " --> pdb=" O ASP L 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP L 135 " --> pdb=" O ILE L 139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 166 through 171 Processing sheet with id=AF8, first strand: chain 'L' and resid 242 through 246 Processing sheet with id=AF9, first strand: chain 'M' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP M 135 " --> pdb=" O ILE M 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 166 through 171 Processing sheet with id=AG2, first strand: chain 'M' and resid 242 through 246 Processing sheet with id=AG3, first strand: chain 'N' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE N 139 " --> pdb=" O ASP N 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP N 135 " --> pdb=" O ILE N 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 166 through 171 Processing sheet with id=AG5, first strand: chain 'N' and resid 242 through 246 Processing sheet with id=AG6, first strand: chain 'O' and resid 100 through 104 removed outlier: 3.673A pdb=" N ILE O 139 " --> pdb=" O ASP O 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP O 135 " --> pdb=" O ILE O 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 166 through 171 Processing sheet with id=AG8, first strand: chain 'O' and resid 242 through 246 4296 hydrogen bonds defined for protein. 12033 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: 23.70 Time building geometry restraints manager: 18.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11404 1.32 - 1.44: 11036 1.44 - 1.56: 34080 1.56 - 1.68: 0 1.68 - 1.80: 390 Bond restraints: 56910 Sorted by residual: bond pdb=" C SER O 437 " pdb=" O SER O 437 " ideal model delta sigma weight residual 1.248 1.209 0.040 1.26e-02 6.30e+03 9.95e+00 bond pdb=" C SER H 437 " pdb=" O SER H 437 " ideal model delta sigma weight residual 1.248 1.209 0.040 1.26e-02 6.30e+03 9.93e+00 bond pdb=" C SER C 437 " pdb=" O SER C 437 " ideal model delta sigma weight residual 1.248 1.209 0.040 1.26e-02 6.30e+03 9.83e+00 bond pdb=" C SER K 437 " pdb=" O SER K 437 " ideal model delta sigma weight residual 1.248 1.209 0.039 1.26e-02 6.30e+03 9.77e+00 bond pdb=" C SER L 437 " pdb=" O SER L 437 " ideal model delta sigma weight residual 1.248 1.209 0.039 1.26e-02 6.30e+03 9.69e+00 ... (remaining 56905 not shown) Histogram of bond angle deviations from ideal: 97.99 - 107.21: 1816 107.21 - 116.42: 38774 116.42 - 125.64: 35955 125.64 - 134.86: 390 134.86 - 144.07: 15 Bond angle restraints: 76950 Sorted by residual: angle pdb=" N ARG L 634 " pdb=" CA ARG L 634 " pdb=" C ARG L 634 " ideal model delta sigma weight residual 109.59 125.42 -15.83 1.61e+00 3.86e-01 9.67e+01 angle pdb=" N ARG G 634 " pdb=" CA ARG G 634 " pdb=" C ARG G 634 " ideal model delta sigma weight residual 109.59 125.40 -15.81 1.61e+00 3.86e-01 9.65e+01 angle pdb=" N ARG C 634 " pdb=" CA ARG C 634 " pdb=" C ARG C 634 " ideal model delta sigma weight residual 109.59 125.39 -15.80 1.61e+00 3.86e-01 9.63e+01 angle pdb=" N ARG B 634 " pdb=" CA ARG B 634 " pdb=" C ARG B 634 " ideal model delta sigma weight residual 109.59 125.38 -15.79 1.61e+00 3.86e-01 9.62e+01 angle pdb=" N ARG N 634 " pdb=" CA ARG N 634 " pdb=" C ARG N 634 " ideal model delta sigma weight residual 109.59 125.37 -15.78 1.61e+00 3.86e-01 9.61e+01 ... (remaining 76945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 33285 16.12 - 32.24: 1665 32.24 - 48.36: 180 48.36 - 64.49: 45 64.49 - 80.61: 75 Dihedral angle restraints: 35250 sinusoidal: 13980 harmonic: 21270 Sorted by residual: dihedral pdb=" CA LEU K 225 " pdb=" C LEU K 225 " pdb=" N LYS K 226 " pdb=" CA LYS K 226 " ideal model delta harmonic sigma weight residual 180.00 151.27 28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA LEU C 225 " pdb=" C LEU C 225 " pdb=" N LYS C 226 " pdb=" CA LYS C 226 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LEU H 225 " pdb=" C LEU H 225 " pdb=" N LYS H 226 " pdb=" CA LYS H 226 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 35247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6089 0.053 - 0.107: 2432 0.107 - 0.160: 723 0.160 - 0.214: 116 0.214 - 0.267: 45 Chirality restraints: 9405 Sorted by residual: chirality pdb=" CA ARG I 633 " pdb=" N ARG I 633 " pdb=" C ARG I 633 " pdb=" CB ARG I 633 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG O 633 " pdb=" N ARG O 633 " pdb=" C ARG O 633 " pdb=" CB ARG O 633 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG C 633 " pdb=" N ARG C 633 " pdb=" C ARG C 633 " pdb=" CB ARG C 633 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 9402 not shown) Planarity restraints: 10020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER M 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO M 438 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO M 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO M 438 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO G 438 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO G 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO G 438 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 437 " 0.090 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO I 438 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO I 438 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO I 438 " 0.071 5.00e-02 4.00e+02 ... (remaining 10017 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 180 2.30 - 2.95: 27246 2.95 - 3.60: 79130 3.60 - 4.25: 125487 4.25 - 4.90: 219619 Nonbonded interactions: 451662 Sorted by model distance: nonbonded pdb=" SD MET E 236 " pdb=" O ARG F 209 " model vdw 1.654 3.400 nonbonded pdb=" SD MET I 236 " pdb=" O ARG J 209 " model vdw 1.654 3.400 nonbonded pdb=" SD MET B 236 " pdb=" O ARG C 209 " model vdw 1.654 3.400 nonbonded pdb=" SD MET L 236 " pdb=" O ARG M 209 " model vdw 1.655 3.400 nonbonded pdb=" SD MET D 236 " pdb=" O ARG E 209 " model vdw 1.655 3.400 ... (remaining 451657 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 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: 0.040 Extract box with map and model: 12.590 Check model and map are aligned: 0.620 Set scattering table: 0.410 Process input model: 117.990 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 0.092 56910 Z= 0.582 Angle : 1.175 17.073 76950 Z= 0.658 Chirality : 0.064 0.267 9405 Planarity : 0.007 0.139 10020 Dihedral : 10.834 80.607 21450 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 27.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.08), residues: 7290 helix: -2.39 (0.10), residues: 1860 sheet: -1.56 (0.07), residues: 3255 loop : -1.17 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 341 HIS 0.004 0.001 HIS O 288 PHE 0.015 0.003 PHE E 580 TYR 0.035 0.003 TYR F 134 ARG 0.010 0.002 ARG O 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1043 time to evaluate : 4.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8937 (m-30) cc_final: 0.8610 (m-30) REVERT: A 303 MET cc_start: 0.8035 (tpp) cc_final: 0.7681 (tpp) REVERT: A 323 GLU cc_start: 0.8605 (tt0) cc_final: 0.8363 (tt0) REVERT: A 336 ASN cc_start: 0.8138 (t0) cc_final: 0.7873 (m-40) REVERT: A 397 TYR cc_start: 0.8406 (m-80) cc_final: 0.8098 (m-80) REVERT: A 533 GLN cc_start: 0.8848 (mt0) cc_final: 0.8641 (mp10) REVERT: A 543 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8418 (mt-10) REVERT: A 547 GLU cc_start: 0.8468 (tt0) cc_final: 0.8213 (tm-30) REVERT: A 593 ASP cc_start: 0.8654 (t70) cc_final: 0.8395 (t0) REVERT: B 290 ASP cc_start: 0.9007 (m-30) cc_final: 0.8783 (m-30) REVERT: B 303 MET cc_start: 0.8063 (tpp) cc_final: 0.7467 (tpp) REVERT: B 397 TYR cc_start: 0.8309 (m-80) cc_final: 0.8041 (m-80) REVERT: B 399 LYS cc_start: 0.8558 (mttm) cc_final: 0.8311 (tptm) REVERT: B 416 MET cc_start: 0.6754 (ptm) cc_final: 0.6542 (ptp) REVERT: B 436 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.7978 (p) REVERT: B 533 GLN cc_start: 0.8894 (mt0) cc_final: 0.8636 (mp10) REVERT: B 593 ASP cc_start: 0.8497 (t70) cc_final: 0.8018 (t0) REVERT: B 635 HIS cc_start: 0.7204 (m90) cc_final: 0.6680 (m-70) REVERT: C 290 ASP cc_start: 0.8985 (m-30) cc_final: 0.8769 (m-30) REVERT: C 303 MET cc_start: 0.7843 (tpp) cc_final: 0.7026 (tpp) REVERT: C 368 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8213 (mm-30) REVERT: C 374 GLN cc_start: 0.6931 (tt0) cc_final: 0.6322 (tm-30) REVERT: C 407 ILE cc_start: 0.9072 (mm) cc_final: 0.8823 (mt) REVERT: C 533 GLN cc_start: 0.8941 (mt0) cc_final: 0.8734 (mm-40) REVERT: C 547 GLU cc_start: 0.8392 (tt0) cc_final: 0.8191 (tm-30) REVERT: C 574 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8121 (ttmm) REVERT: C 593 ASP cc_start: 0.8589 (t70) cc_final: 0.8335 (t0) REVERT: C 609 PHE cc_start: 0.8403 (t80) cc_final: 0.8082 (t80) REVERT: C 640 GLN cc_start: 0.6717 (tp40) cc_final: 0.6422 (tp-100) REVERT: D 290 ASP cc_start: 0.8904 (m-30) cc_final: 0.8582 (m-30) REVERT: D 303 MET cc_start: 0.8088 (tpp) cc_final: 0.7359 (tpp) REVERT: D 323 GLU cc_start: 0.8685 (tt0) cc_final: 0.8214 (mt-10) REVERT: D 374 GLN cc_start: 0.6912 (tt0) cc_final: 0.6550 (tm-30) REVERT: D 397 TYR cc_start: 0.8533 (m-80) cc_final: 0.8290 (m-80) REVERT: D 406 SER cc_start: 0.9235 (m) cc_final: 0.9015 (p) REVERT: D 533 GLN cc_start: 0.8805 (mt0) cc_final: 0.8481 (mm-40) REVERT: D 547 GLU cc_start: 0.8478 (tt0) cc_final: 0.8234 (tp30) REVERT: D 574 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8302 (ttmm) REVERT: D 593 ASP cc_start: 0.8702 (t70) cc_final: 0.8491 (t0) REVERT: E 290 ASP cc_start: 0.8938 (m-30) cc_final: 0.8623 (m-30) REVERT: E 303 MET cc_start: 0.7905 (tpp) cc_final: 0.7368 (tpp) REVERT: E 335 ILE cc_start: 0.8843 (mt) cc_final: 0.8605 (mt) REVERT: E 407 ILE cc_start: 0.9164 (mm) cc_final: 0.8899 (mt) REVERT: E 478 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8742 (mttm) REVERT: E 533 GLN cc_start: 0.8899 (mt0) cc_final: 0.8659 (mm-40) REVERT: E 593 ASP cc_start: 0.8656 (t70) cc_final: 0.8192 (t0) REVERT: F 290 ASP cc_start: 0.8880 (m-30) cc_final: 0.8597 (m-30) REVERT: F 368 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8127 (mm-30) REVERT: F 397 TYR cc_start: 0.8402 (m-80) cc_final: 0.8056 (m-80) REVERT: F 407 ILE cc_start: 0.9072 (mm) cc_final: 0.8786 (mt) REVERT: F 485 LYS cc_start: 0.8630 (tttm) cc_final: 0.8239 (tptt) REVERT: F 533 GLN cc_start: 0.8946 (mt0) cc_final: 0.8728 (mm-40) REVERT: F 574 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8385 (ttmm) REVERT: F 593 ASP cc_start: 0.8101 (t70) cc_final: 0.7746 (t0) REVERT: G 303 MET cc_start: 0.7843 (tpp) cc_final: 0.7048 (tpp) REVERT: G 336 ASN cc_start: 0.8106 (t0) cc_final: 0.7847 (t0) REVERT: G 374 GLN cc_start: 0.6924 (tt0) cc_final: 0.6571 (tm-30) REVERT: G 399 LYS cc_start: 0.8564 (mttm) cc_final: 0.8357 (tptm) REVERT: G 406 SER cc_start: 0.9337 (m) cc_final: 0.9135 (p) REVERT: G 436 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8364 (p) REVERT: G 533 GLN cc_start: 0.8854 (mt0) cc_final: 0.8628 (mm-40) REVERT: G 543 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8535 (mt-10) REVERT: G 547 GLU cc_start: 0.8504 (tt0) cc_final: 0.8229 (tm-30) REVERT: G 593 ASP cc_start: 0.8470 (t70) cc_final: 0.8120 (t0) REVERT: G 609 PHE cc_start: 0.8252 (t80) cc_final: 0.7705 (t80) REVERT: H 290 ASP cc_start: 0.8910 (m-30) cc_final: 0.8572 (m-30) REVERT: H 363 MET cc_start: 0.8250 (mtm) cc_final: 0.8013 (mtm) REVERT: H 368 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8295 (mm-30) REVERT: H 478 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8612 (mttp) REVERT: H 533 GLN cc_start: 0.8945 (mt0) cc_final: 0.8612 (mp10) REVERT: H 541 ILE cc_start: 0.9017 (mt) cc_final: 0.8790 (mt) REVERT: H 547 GLU cc_start: 0.8495 (tt0) cc_final: 0.8250 (tm-30) REVERT: I 290 ASP cc_start: 0.8944 (m-30) cc_final: 0.8649 (m-30) REVERT: I 323 GLU cc_start: 0.8624 (tt0) cc_final: 0.8325 (tt0) REVERT: I 368 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8030 (mm-30) REVERT: I 374 GLN cc_start: 0.6696 (tt0) cc_final: 0.6252 (tm-30) REVERT: I 397 TYR cc_start: 0.8660 (m-80) cc_final: 0.8244 (m-80) REVERT: I 406 SER cc_start: 0.9408 (m) cc_final: 0.9126 (p) REVERT: I 436 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8252 (p) REVERT: I 478 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8682 (mttp) REVERT: I 547 GLU cc_start: 0.8670 (tt0) cc_final: 0.8463 (tm-30) REVERT: J 290 ASP cc_start: 0.8860 (m-30) cc_final: 0.8627 (m-30) REVERT: J 303 MET cc_start: 0.8087 (tpp) cc_final: 0.7559 (tpp) REVERT: J 323 GLU cc_start: 0.8546 (tt0) cc_final: 0.8139 (mt-10) REVERT: J 374 GLN cc_start: 0.7011 (tt0) cc_final: 0.6792 (tm-30) REVERT: J 407 ILE cc_start: 0.9193 (mm) cc_final: 0.8922 (mt) REVERT: J 533 GLN cc_start: 0.8975 (mt0) cc_final: 0.8696 (mt0) REVERT: J 543 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8469 (mt-10) REVERT: J 547 GLU cc_start: 0.8272 (tt0) cc_final: 0.7988 (tm-30) REVERT: J 593 ASP cc_start: 0.8505 (t70) cc_final: 0.8239 (t0) REVERT: K 290 ASP cc_start: 0.8742 (m-30) cc_final: 0.8436 (m-30) REVERT: K 303 MET cc_start: 0.7923 (tpp) cc_final: 0.7372 (tpp) REVERT: K 368 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8131 (mm-30) REVERT: K 374 GLN cc_start: 0.6952 (tt0) cc_final: 0.6429 (tm-30) REVERT: K 399 LYS cc_start: 0.8698 (mttm) cc_final: 0.8442 (tptm) REVERT: K 478 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8561 (mttm) REVERT: K 547 GLU cc_start: 0.8467 (tt0) cc_final: 0.8206 (tm-30) REVERT: K 593 ASP cc_start: 0.8313 (t70) cc_final: 0.7737 (t0) REVERT: L 290 ASP cc_start: 0.8908 (m-30) cc_final: 0.8607 (m-30) REVERT: L 397 TYR cc_start: 0.8622 (m-80) cc_final: 0.8278 (m-80) REVERT: L 478 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8792 (mttm) REVERT: L 479 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8066 (mt-10) REVERT: L 533 GLN cc_start: 0.8860 (mt0) cc_final: 0.8569 (mm-40) REVERT: L 593 ASP cc_start: 0.8731 (t70) cc_final: 0.8293 (t0) REVERT: L 616 ARG cc_start: 0.6456 (mtm-85) cc_final: 0.6103 (mtt90) REVERT: M 303 MET cc_start: 0.7968 (tpp) cc_final: 0.7395 (tpp) REVERT: M 336 ASN cc_start: 0.8011 (t0) cc_final: 0.7789 (t0) REVERT: M 374 GLN cc_start: 0.6790 (tt0) cc_final: 0.6510 (tm-30) REVERT: M 407 ILE cc_start: 0.9136 (mm) cc_final: 0.8895 (mt) REVERT: M 436 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8251 (p) REVERT: M 533 GLN cc_start: 0.8837 (mt0) cc_final: 0.8562 (mp10) REVERT: M 593 ASP cc_start: 0.8614 (t70) cc_final: 0.8212 (t0) REVERT: N 290 ASP cc_start: 0.8942 (m-30) cc_final: 0.8610 (m-30) REVERT: N 303 MET cc_start: 0.8021 (tpp) cc_final: 0.7606 (mmm) REVERT: N 354 ASN cc_start: 0.8955 (m110) cc_final: 0.8610 (m110) REVERT: N 368 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7992 (mm-30) REVERT: N 397 TYR cc_start: 0.8480 (m-80) cc_final: 0.8049 (m-80) REVERT: N 407 ILE cc_start: 0.9171 (mm) cc_final: 0.8884 (mt) REVERT: N 478 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8634 (mttm) REVERT: N 533 GLN cc_start: 0.8838 (mt0) cc_final: 0.8556 (mm-40) REVERT: N 547 GLU cc_start: 0.8599 (tt0) cc_final: 0.8382 (tt0) REVERT: N 573 GLU cc_start: 0.8262 (tt0) cc_final: 0.8002 (tt0) REVERT: N 593 ASP cc_start: 0.8538 (t70) cc_final: 0.8104 (t0) REVERT: O 290 ASP cc_start: 0.8882 (m-30) cc_final: 0.8580 (m-30) REVERT: O 303 MET cc_start: 0.7868 (tpp) cc_final: 0.6964 (tpp) REVERT: O 436 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8397 (p) REVERT: O 478 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8761 (mttp) REVERT: O 528 MET cc_start: 0.8949 (ttm) cc_final: 0.8725 (ttm) REVERT: O 533 GLN cc_start: 0.8965 (mt0) cc_final: 0.8621 (mm110) REVERT: O 593 ASP cc_start: 0.8333 (t70) cc_final: 0.7936 (t0) outliers start: 15 outliers final: 10 residues processed: 1058 average time/residue: 0.5623 time to fit residues: 972.9367 Evaluate side-chains 659 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 644 time to evaluate : 4.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 436 SER Chi-restraints excluded: chain F residue 436 SER Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain H residue 436 SER Chi-restraints excluded: chain I residue 436 SER Chi-restraints excluded: chain J residue 436 SER Chi-restraints excluded: chain K residue 436 SER Chi-restraints excluded: chain L residue 436 SER Chi-restraints excluded: chain M residue 436 SER Chi-restraints excluded: chain N residue 436 SER Chi-restraints excluded: chain O residue 436 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 0.3980 chunk 557 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 375 optimal weight: 0.5980 chunk 297 optimal weight: 20.0000 chunk 576 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 428 optimal weight: 0.9990 chunk 667 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 288 HIS A 300 GLN A 340 GLN A 424 ASN A 428 ASN A 502 GLN A 640 GLN B 242 ASN B 288 HIS B 300 GLN B 340 GLN B 424 ASN B 428 ASN B 502 GLN B 640 GLN C 288 HIS C 300 GLN C 340 GLN C 354 ASN C 428 ASN C 502 GLN C 640 GLN D 288 HIS D 300 GLN D 340 GLN D 354 ASN D 424 ASN D 428 ASN D 499 ASN D 502 GLN D 640 GLN E 242 ASN E 288 HIS E 300 GLN E 340 GLN E 424 ASN E 428 ASN E 640 GLN F 288 HIS F 300 GLN F 340 GLN F 424 ASN F 428 ASN F 502 GLN F 640 GLN G 242 ASN G 288 HIS G 300 GLN G 340 GLN G 424 ASN G 428 ASN G 502 GLN G 640 GLN H 288 HIS H 300 GLN H 340 GLN H 354 ASN H 424 ASN H 428 ASN H 499 ASN I 288 HIS I 300 GLN I 340 GLN I 424 ASN I 428 ASN I 502 GLN I 640 GLN J 242 ASN J 288 HIS J 300 GLN J 336 ASN J 340 GLN J 424 ASN J 428 ASN J 640 GLN K 242 ASN K 288 HIS K 300 GLN K 340 GLN K 424 ASN K 428 ASN K 502 GLN L 288 HIS L 340 GLN L 424 ASN L 428 ASN L 502 GLN L 640 GLN M 242 ASN M 288 HIS M 300 GLN M 340 GLN M 424 ASN M 428 ASN M 499 ASN M 502 GLN M 640 GLN N 288 HIS N 300 GLN N 340 GLN N 428 ASN N 502 GLN N 640 GLN O 288 HIS O 300 GLN O 340 GLN O 354 ASN O 424 ASN O 428 ASN O 502 GLN O 640 GLN Total number of N/Q/H flips: 112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 56910 Z= 0.258 Angle : 0.706 8.400 76950 Z= 0.372 Chirality : 0.050 0.172 9405 Planarity : 0.005 0.075 10020 Dihedral : 6.125 23.096 7875 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.52 % Allowed : 8.51 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -1.62 (0.09), residues: 7290 helix: -0.70 (0.11), residues: 2130 sheet: -1.07 (0.08), residues: 3210 loop : -0.96 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 341 HIS 0.004 0.002 HIS A 635 PHE 0.013 0.002 PHE H 609 TYR 0.017 0.002 TYR G 134 ARG 0.010 0.000 ARG K 616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 811 time to evaluate : 4.816 Fit side-chains REVERT: A 284 MET cc_start: 0.8390 (tpp) cc_final: 0.8162 (tpp) REVERT: A 290 ASP cc_start: 0.8883 (m-30) cc_final: 0.8595 (m-30) REVERT: A 303 MET cc_start: 0.8021 (tpp) cc_final: 0.7300 (tpp) REVERT: A 368 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8077 (mt-10) REVERT: A 543 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8410 (mt-10) REVERT: A 552 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7470 (m) REVERT: B 303 MET cc_start: 0.7893 (tpp) cc_final: 0.7352 (tpp) REVERT: B 533 GLN cc_start: 0.8847 (mt0) cc_final: 0.8614 (mp10) REVERT: B 543 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 547 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: B 593 ASP cc_start: 0.8282 (t70) cc_final: 0.7949 (t0) REVERT: C 290 ASP cc_start: 0.8946 (m-30) cc_final: 0.8732 (m-30) REVERT: C 303 MET cc_start: 0.7774 (tpp) cc_final: 0.6867 (tpp) REVERT: C 374 GLN cc_start: 0.6846 (tt0) cc_final: 0.6332 (tm-30) REVERT: C 424 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8088 (p0) REVERT: C 447 GLU cc_start: 0.8783 (pt0) cc_final: 0.8500 (pt0) REVERT: C 533 GLN cc_start: 0.8873 (mt0) cc_final: 0.8625 (mm110) REVERT: C 574 LYS cc_start: 0.8427 (ttmt) cc_final: 0.8076 (mtpp) REVERT: C 593 ASP cc_start: 0.8535 (t70) cc_final: 0.8218 (t0) REVERT: D 301 ASP cc_start: 0.8370 (p0) cc_final: 0.8119 (p0) REVERT: D 303 MET cc_start: 0.8037 (tpp) cc_final: 0.7516 (tpp) REVERT: D 323 GLU cc_start: 0.8580 (tt0) cc_final: 0.8319 (mt-10) REVERT: D 374 GLN cc_start: 0.6679 (tt0) cc_final: 0.6449 (tm-30) REVERT: D 547 GLU cc_start: 0.8164 (tt0) cc_final: 0.7869 (tm-30) REVERT: D 574 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8334 (ttmm) REVERT: E 290 ASP cc_start: 0.8904 (m-30) cc_final: 0.8577 (m-30) REVERT: E 303 MET cc_start: 0.7810 (tpp) cc_final: 0.7353 (tpp) REVERT: E 407 ILE cc_start: 0.9167 (mm) cc_final: 0.8952 (mt) REVERT: E 533 GLN cc_start: 0.8879 (mt0) cc_final: 0.8678 (mp10) REVERT: E 593 ASP cc_start: 0.8543 (t70) cc_final: 0.8029 (t0) REVERT: F 290 ASP cc_start: 0.8778 (m-30) cc_final: 0.8567 (m-30) REVERT: F 331 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7941 (tt0) REVERT: F 368 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8072 (mt-10) REVERT: F 407 ILE cc_start: 0.9114 (mm) cc_final: 0.8743 (mt) REVERT: F 485 LYS cc_start: 0.8571 (tttm) cc_final: 0.8158 (tptt) REVERT: G 303 MET cc_start: 0.7759 (tpp) cc_final: 0.7191 (tpp) REVERT: G 368 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8077 (mm-30) REVERT: G 543 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8412 (mt-10) REVERT: G 593 ASP cc_start: 0.8203 (t70) cc_final: 0.7808 (t0) REVERT: H 290 ASP cc_start: 0.8902 (m-30) cc_final: 0.8646 (m-30) REVERT: H 303 MET cc_start: 0.7898 (tpp) cc_final: 0.6978 (tpp) REVERT: H 363 MET cc_start: 0.8136 (mtm) cc_final: 0.7892 (mtm) REVERT: H 368 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8252 (mt-10) REVERT: H 478 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8680 (mttp) REVERT: H 479 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8478 (mt-10) REVERT: H 524 ASN cc_start: 0.8636 (p0) cc_final: 0.8345 (p0) REVERT: H 533 GLN cc_start: 0.8876 (mt0) cc_final: 0.8629 (mp10) REVERT: H 541 ILE cc_start: 0.8730 (mt) cc_final: 0.8516 (mt) REVERT: I 290 ASP cc_start: 0.8899 (m-30) cc_final: 0.8621 (m-30) REVERT: I 300 GLN cc_start: 0.7004 (tp-100) cc_final: 0.6776 (tp40) REVERT: I 368 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7831 (mt-10) REVERT: I 374 GLN cc_start: 0.6274 (tt0) cc_final: 0.5896 (tm-30) REVERT: I 406 SER cc_start: 0.9304 (m) cc_final: 0.9044 (p) REVERT: J 303 MET cc_start: 0.7789 (tpp) cc_final: 0.7379 (tpp) REVERT: J 323 GLU cc_start: 0.8444 (tt0) cc_final: 0.8236 (tt0) REVERT: J 368 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8056 (mt-10) REVERT: J 407 ILE cc_start: 0.9218 (mm) cc_final: 0.8932 (mt) REVERT: J 552 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7257 (t) REVERT: K 303 MET cc_start: 0.7880 (tpp) cc_final: 0.7383 (tpp) REVERT: K 368 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8079 (mm-30) REVERT: K 374 GLN cc_start: 0.6731 (tt0) cc_final: 0.6382 (tm-30) REVERT: K 399 LYS cc_start: 0.8676 (mttm) cc_final: 0.8449 (tptm) REVERT: K 478 LYS cc_start: 0.8932 (mtpp) cc_final: 0.8645 (mttp) REVERT: K 546 LEU cc_start: 0.8664 (mp) cc_final: 0.8450 (mt) REVERT: L 290 ASP cc_start: 0.8848 (m-30) cc_final: 0.8577 (m-30) REVERT: L 303 MET cc_start: 0.7933 (tpp) cc_final: 0.7711 (tpp) REVERT: L 478 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8871 (mttm) REVERT: L 533 GLN cc_start: 0.8790 (mt0) cc_final: 0.8488 (mm-40) REVERT: L 534 MET cc_start: 0.9167 (ttm) cc_final: 0.8924 (ttm) REVERT: L 593 ASP cc_start: 0.8596 (t70) cc_final: 0.8136 (t0) REVERT: M 303 MET cc_start: 0.7750 (tpp) cc_final: 0.7218 (tpp) REVERT: M 337 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7952 (pt) REVERT: M 374 GLN cc_start: 0.6699 (tt0) cc_final: 0.6462 (tm-30) REVERT: M 397 TYR cc_start: 0.8604 (m-80) cc_final: 0.8296 (m-80) REVERT: M 476 ASP cc_start: 0.8167 (t70) cc_final: 0.7951 (t70) REVERT: M 501 GLU cc_start: 0.8250 (tt0) cc_final: 0.8032 (mp0) REVERT: M 533 GLN cc_start: 0.8834 (mt0) cc_final: 0.8633 (mp10) REVERT: N 290 ASP cc_start: 0.8761 (m-30) cc_final: 0.8512 (m-30) REVERT: N 368 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8076 (mt-10) REVERT: N 407 ILE cc_start: 0.9188 (mm) cc_final: 0.8901 (mt) REVERT: N 547 GLU cc_start: 0.8241 (tt0) cc_final: 0.7996 (mm-30) REVERT: N 606 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7877 (mm-30) REVERT: O 290 ASP cc_start: 0.8873 (m-30) cc_final: 0.8631 (m-30) REVERT: O 303 MET cc_start: 0.8085 (tpp) cc_final: 0.7205 (tpp) REVERT: O 368 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8117 (mt-10) REVERT: O 533 GLN cc_start: 0.8910 (mt0) cc_final: 0.8675 (mp10) outliers start: 157 outliers final: 57 residues processed: 936 average time/residue: 0.4993 time to fit residues: 805.5390 Evaluate side-chains 692 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 630 time to evaluate : 4.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 552 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 402 SER Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 301 ASP Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 514 VAL Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 402 SER Chi-restraints excluded: chain O residue 552 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 555 optimal weight: 1.9990 chunk 454 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 668 optimal weight: 0.0050 chunk 722 optimal weight: 0.2980 chunk 595 optimal weight: 7.9990 chunk 663 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 536 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 ASN C 242 ASN C 511 ASN D 242 ASN ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN E 511 ASN F 242 ASN G 511 ASN H 242 ASN H 511 ASN I 242 ASN I 511 ASN J 511 ASN L 242 ASN ** L 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 GLN M 511 ASN N 242 ASN N 354 ASN O 242 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 56910 Z= 0.261 Angle : 0.644 9.848 76950 Z= 0.337 Chirality : 0.050 0.232 9405 Planarity : 0.004 0.064 10020 Dihedral : 5.527 20.661 7860 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.89 % Allowed : 9.46 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -0.93 (0.09), residues: 7290 helix: 0.30 (0.11), residues: 2145 sheet: -0.80 (0.08), residues: 3240 loop : -0.89 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 419 HIS 0.002 0.001 HIS I 635 PHE 0.023 0.001 PHE E 609 TYR 0.012 0.002 TYR E 352 ARG 0.005 0.000 ARG I 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 721 time to evaluate : 6.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: -0.0446 (OUTLIER) cc_final: -0.0710 (mp) REVERT: A 300 GLN cc_start: 0.7394 (tp-100) cc_final: 0.7043 (tp40) REVERT: A 303 MET cc_start: 0.8053 (tpp) cc_final: 0.7206 (tpp) REVERT: A 447 GLU cc_start: 0.8707 (pt0) cc_final: 0.8415 (pm20) REVERT: A 543 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 593 ASP cc_start: 0.8391 (t70) cc_final: 0.8040 (t0) REVERT: B 303 MET cc_start: 0.7995 (tpp) cc_final: 0.7345 (tpp) REVERT: B 370 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7902 (mtmm) REVERT: B 416 MET cc_start: 0.7572 (pmm) cc_final: 0.7353 (pmm) REVERT: B 511 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8109 (p0) REVERT: B 533 GLN cc_start: 0.8930 (mt0) cc_final: 0.8687 (mp10) REVERT: B 536 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8967 (p) REVERT: B 543 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8507 (mt-10) REVERT: B 547 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8221 (mm-30) REVERT: B 593 ASP cc_start: 0.8418 (t70) cc_final: 0.8025 (t0) REVERT: C 118 LEU cc_start: -0.0344 (OUTLIER) cc_final: -0.0545 (mp) REVERT: C 303 MET cc_start: 0.8066 (tpp) cc_final: 0.6969 (tpp) REVERT: C 407 ILE cc_start: 0.9166 (mm) cc_final: 0.8930 (mt) REVERT: C 416 MET cc_start: 0.7180 (pmm) cc_final: 0.6964 (pmm) REVERT: C 424 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8173 (p0) REVERT: C 533 GLN cc_start: 0.8886 (mt0) cc_final: 0.8674 (mm110) REVERT: C 573 GLU cc_start: 0.8078 (tt0) cc_final: 0.7831 (mt-10) REVERT: C 574 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8156 (mtpp) REVERT: C 593 ASP cc_start: 0.8593 (t70) cc_final: 0.8203 (t0) REVERT: D 301 ASP cc_start: 0.8393 (p0) cc_final: 0.8109 (p0) REVERT: D 303 MET cc_start: 0.8112 (tpp) cc_final: 0.7508 (tpp) REVERT: D 323 GLU cc_start: 0.8627 (tt0) cc_final: 0.8313 (mt-10) REVERT: D 374 GLN cc_start: 0.6651 (tt0) cc_final: 0.6388 (tm-30) REVERT: D 501 GLU cc_start: 0.8328 (tt0) cc_final: 0.8087 (mt-10) REVERT: D 547 GLU cc_start: 0.8250 (tt0) cc_final: 0.7919 (tm-30) REVERT: D 574 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8347 (ttmm) REVERT: E 118 LEU cc_start: 0.0004 (OUTLIER) cc_final: -0.0298 (mp) REVERT: E 290 ASP cc_start: 0.8813 (m-30) cc_final: 0.8598 (m-30) REVERT: E 303 MET cc_start: 0.7892 (tpp) cc_final: 0.7284 (tpp) REVERT: E 593 ASP cc_start: 0.8404 (t70) cc_final: 0.7943 (t0) REVERT: F 118 LEU cc_start: 0.0419 (OUTLIER) cc_final: 0.0197 (mp) REVERT: F 368 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8054 (mt-10) REVERT: F 407 ILE cc_start: 0.9160 (mm) cc_final: 0.8827 (mt) REVERT: F 485 LYS cc_start: 0.8516 (tttm) cc_final: 0.8132 (tptt) REVERT: F 536 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8973 (p) REVERT: F 547 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: G 284 MET cc_start: 0.8356 (tpp) cc_final: 0.7917 (mpp) REVERT: G 303 MET cc_start: 0.7881 (tpp) cc_final: 0.7184 (tpp) REVERT: G 374 GLN cc_start: 0.5252 (tm-30) cc_final: 0.4977 (tm-30) REVERT: G 447 GLU cc_start: 0.8819 (pt0) cc_final: 0.8386 (pm20) REVERT: G 543 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8468 (mt-10) REVERT: G 593 ASP cc_start: 0.8225 (t70) cc_final: 0.7777 (t0) REVERT: H 118 LEU cc_start: -0.0307 (OUTLIER) cc_final: -0.0530 (mp) REVERT: H 303 MET cc_start: 0.7959 (tpp) cc_final: 0.6927 (tpp) REVERT: H 363 MET cc_start: 0.8142 (mtm) cc_final: 0.7880 (mtm) REVERT: H 368 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8245 (mt-10) REVERT: H 478 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8639 (mttp) REVERT: H 524 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8371 (p0) REVERT: H 533 GLN cc_start: 0.8903 (mt0) cc_final: 0.8659 (mp10) REVERT: H 638 GLU cc_start: 0.7818 (tp30) cc_final: 0.7573 (tp30) REVERT: I 300 GLN cc_start: 0.7415 (tp-100) cc_final: 0.7155 (tp40) REVERT: I 368 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7765 (mt-10) REVERT: I 374 GLN cc_start: 0.6256 (tt0) cc_final: 0.5815 (tm-30) REVERT: I 397 TYR cc_start: 0.8426 (m-80) cc_final: 0.7956 (m-80) REVERT: I 406 SER cc_start: 0.9304 (m) cc_final: 0.9054 (p) REVERT: I 424 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8210 (p0) REVERT: J 303 MET cc_start: 0.7893 (tpp) cc_final: 0.7369 (tpp) REVERT: J 323 GLU cc_start: 0.8511 (tt0) cc_final: 0.8243 (tt0) REVERT: J 328 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7955 (mt-10) REVERT: J 368 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8054 (mt-10) REVERT: J 501 GLU cc_start: 0.8304 (tt0) cc_final: 0.7996 (mt-10) REVERT: J 593 ASP cc_start: 0.8156 (t70) cc_final: 0.7954 (t0) REVERT: K 245 VAL cc_start: 0.8886 (p) cc_final: 0.8679 (m) REVERT: K 284 MET cc_start: 0.8359 (tpp) cc_final: 0.8152 (mpp) REVERT: K 303 MET cc_start: 0.7912 (tpp) cc_final: 0.7663 (tpp) REVERT: K 368 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8058 (mm-30) REVERT: K 374 GLN cc_start: 0.6723 (tt0) cc_final: 0.6316 (tm-30) REVERT: K 399 LYS cc_start: 0.8675 (mttm) cc_final: 0.8453 (tptm) REVERT: K 416 MET cc_start: 0.7598 (pmm) cc_final: 0.7365 (pmm) REVERT: K 478 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8652 (mttp) REVERT: K 524 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8353 (p0) REVERT: K 606 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8294 (mm-30) REVERT: L 303 MET cc_start: 0.8085 (tpp) cc_final: 0.7831 (tpp) REVERT: L 447 GLU cc_start: 0.8616 (pt0) cc_final: 0.8301 (pm20) REVERT: L 478 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8856 (mttm) REVERT: L 533 GLN cc_start: 0.8851 (mt0) cc_final: 0.8572 (mm-40) REVERT: L 593 ASP cc_start: 0.8613 (t70) cc_final: 0.8180 (t0) REVERT: M 294 LEU cc_start: 0.8944 (pp) cc_final: 0.8670 (pt) REVERT: M 303 MET cc_start: 0.7911 (tpp) cc_final: 0.7263 (tpp) REVERT: M 337 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7947 (pt) REVERT: M 374 GLN cc_start: 0.6605 (tt0) cc_final: 0.6404 (tm-30) REVERT: M 397 TYR cc_start: 0.8661 (m-80) cc_final: 0.8286 (m-80) REVERT: M 416 MET cc_start: 0.7548 (pmm) cc_final: 0.7257 (pmm) REVERT: M 424 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.7958 (p0) REVERT: M 476 ASP cc_start: 0.8173 (t70) cc_final: 0.7972 (t70) REVERT: M 501 GLU cc_start: 0.8219 (tt0) cc_final: 0.7894 (mt-10) REVERT: M 533 GLN cc_start: 0.8836 (mt0) cc_final: 0.8590 (mp10) REVERT: M 612 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7294 (mm-30) REVERT: N 118 LEU cc_start: -0.0323 (OUTLIER) cc_final: -0.0634 (mp) REVERT: N 284 MET cc_start: 0.8611 (tpp) cc_final: 0.8141 (mpp) REVERT: N 290 ASP cc_start: 0.8796 (m-30) cc_final: 0.8557 (m-30) REVERT: N 303 MET cc_start: 0.7835 (tpp) cc_final: 0.7564 (tpp) REVERT: N 501 GLU cc_start: 0.8318 (tt0) cc_final: 0.7950 (mt-10) REVERT: O 303 MET cc_start: 0.8207 (tpp) cc_final: 0.7202 (tpp) REVERT: O 368 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8130 (mt-10) REVERT: O 424 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8122 (p0) REVERT: O 533 GLN cc_start: 0.8945 (mt0) cc_final: 0.8697 (mm110) REVERT: O 616 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7208 (mtt90) outliers start: 242 outliers final: 107 residues processed: 935 average time/residue: 0.4903 time to fit residues: 800.2224 Evaluate side-chains 775 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 649 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 511 ASN Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 524 ASN Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 424 ASN Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 254 ASP Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 524 ASN Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 402 SER Chi-restraints excluded: chain L residue 424 ASN Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 301 ASP Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 424 ASN Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 524 ASN Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain O residue 218 ASP Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 402 SER Chi-restraints excluded: chain O residue 424 ASN Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 536 VAL Chi-restraints excluded: chain O residue 552 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 3.9990 chunk 502 optimal weight: 0.3980 chunk 347 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 449 optimal weight: 9.9990 chunk 671 optimal weight: 0.7980 chunk 710 optimal weight: 9.9990 chunk 350 optimal weight: 3.9990 chunk 636 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 635 HIS ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 GLN F 424 ASN J 336 ASN ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 GLN L 502 GLN M 511 ASN N 242 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 56910 Z= 0.355 Angle : 0.649 8.617 76950 Z= 0.342 Chirality : 0.050 0.269 9405 Planarity : 0.005 0.058 10020 Dihedral : 5.426 21.667 7860 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.34 % Allowed : 10.81 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -0.67 (0.09), residues: 7290 helix: 0.86 (0.11), residues: 2040 sheet: -0.77 (0.08), residues: 3315 loop : -0.88 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 419 HIS 0.003 0.001 HIS F 635 PHE 0.018 0.001 PHE G 609 TYR 0.010 0.002 TYR G 134 ARG 0.006 0.000 ARG K 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 661 time to evaluate : 4.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: -0.0710 (OUTLIER) cc_final: -0.0949 (mp) REVERT: A 300 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7193 (tp40) REVERT: A 303 MET cc_start: 0.8126 (tpp) cc_final: 0.7203 (tpp) REVERT: A 543 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 552 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7312 (m) REVERT: A 593 ASP cc_start: 0.8371 (t70) cc_final: 0.8139 (t0) REVERT: B 303 MET cc_start: 0.8002 (tpp) cc_final: 0.7242 (tpp) REVERT: B 370 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7852 (mtmm) REVERT: B 524 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8535 (p0) REVERT: B 533 GLN cc_start: 0.8980 (mt0) cc_final: 0.8710 (mp10) REVERT: B 536 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9038 (p) REVERT: B 543 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8571 (mt-10) REVERT: B 547 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8368 (mm-30) REVERT: B 593 ASP cc_start: 0.8375 (t70) cc_final: 0.7893 (t0) REVERT: B 612 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6574 (tm-30) REVERT: C 284 MET cc_start: 0.8580 (tpp) cc_final: 0.8322 (mpp) REVERT: C 303 MET cc_start: 0.8087 (tpp) cc_final: 0.6894 (tpp) REVERT: C 407 ILE cc_start: 0.9163 (mm) cc_final: 0.8919 (mt) REVERT: C 416 MET cc_start: 0.7133 (pmm) cc_final: 0.6578 (pmm) REVERT: C 533 GLN cc_start: 0.8865 (mt0) cc_final: 0.8594 (mm110) REVERT: C 535 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9018 (tt) REVERT: C 573 GLU cc_start: 0.8102 (tt0) cc_final: 0.7832 (mt-10) REVERT: C 574 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8206 (mtpp) REVERT: C 593 ASP cc_start: 0.8558 (t70) cc_final: 0.8280 (t0) REVERT: D 301 ASP cc_start: 0.8476 (p0) cc_final: 0.8203 (p0) REVERT: D 303 MET cc_start: 0.8082 (tpp) cc_final: 0.7325 (tpp) REVERT: D 374 GLN cc_start: 0.6627 (tt0) cc_final: 0.6361 (tm-30) REVERT: D 501 GLU cc_start: 0.8400 (tt0) cc_final: 0.8140 (mt-10) REVERT: D 502 GLN cc_start: 0.8471 (tm130) cc_final: 0.8170 (tm-30) REVERT: D 547 GLU cc_start: 0.8221 (tt0) cc_final: 0.7907 (tm-30) REVERT: D 574 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8313 (ttmm) REVERT: D 593 ASP cc_start: 0.8438 (t70) cc_final: 0.8121 (t0) REVERT: E 284 MET cc_start: 0.8283 (tpt) cc_final: 0.8008 (tpp) REVERT: E 290 ASP cc_start: 0.8841 (m-30) cc_final: 0.8618 (m-30) REVERT: E 303 MET cc_start: 0.7976 (tpp) cc_final: 0.7266 (tpp) REVERT: E 524 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8653 (p0) REVERT: E 593 ASP cc_start: 0.8364 (t70) cc_final: 0.7890 (t0) REVERT: F 368 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8150 (mt-10) REVERT: F 397 TYR cc_start: 0.8690 (m-80) cc_final: 0.8356 (m-80) REVERT: F 407 ILE cc_start: 0.9188 (mm) cc_final: 0.8837 (mt) REVERT: F 485 LYS cc_start: 0.8525 (tttm) cc_final: 0.8137 (tptt) REVERT: F 547 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: G 303 MET cc_start: 0.7989 (tpp) cc_final: 0.7021 (tpp) REVERT: G 543 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8394 (mt-10) REVERT: G 547 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: G 593 ASP cc_start: 0.8211 (t70) cc_final: 0.7784 (t0) REVERT: H 118 LEU cc_start: -0.0367 (OUTLIER) cc_final: -0.0570 (mp) REVERT: H 303 MET cc_start: 0.7975 (tpp) cc_final: 0.6908 (tpp) REVERT: H 363 MET cc_start: 0.8065 (mtm) cc_final: 0.7798 (mtm) REVERT: H 368 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8163 (mt-10) REVERT: H 414 ILE cc_start: 0.8179 (mt) cc_final: 0.7948 (pt) REVERT: H 478 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8720 (mttp) REVERT: H 533 GLN cc_start: 0.8951 (mt0) cc_final: 0.8692 (mp10) REVERT: H 616 ARG cc_start: 0.7499 (mtt90) cc_final: 0.6941 (ttm110) REVERT: H 638 GLU cc_start: 0.7824 (tp30) cc_final: 0.7556 (tp30) REVERT: I 300 GLN cc_start: 0.7540 (tp-100) cc_final: 0.7163 (tp40) REVERT: I 368 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7851 (mt-10) REVERT: I 374 GLN cc_start: 0.6353 (tt0) cc_final: 0.5887 (tm-30) REVERT: I 407 ILE cc_start: 0.9287 (mm) cc_final: 0.8968 (tp) REVERT: I 533 GLN cc_start: 0.9015 (mt0) cc_final: 0.8752 (mp10) REVERT: J 303 MET cc_start: 0.7936 (tpp) cc_final: 0.7247 (tpp) REVERT: J 323 GLU cc_start: 0.8523 (tt0) cc_final: 0.8230 (tt0) REVERT: J 368 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8035 (mt-10) REVERT: J 501 GLU cc_start: 0.8362 (tt0) cc_final: 0.8117 (mt-10) REVERT: J 543 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8393 (mt-10) REVERT: K 368 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8031 (mm-30) REVERT: K 374 GLN cc_start: 0.6837 (tt0) cc_final: 0.6419 (tm-30) REVERT: K 399 LYS cc_start: 0.8665 (mttm) cc_final: 0.8462 (tptm) REVERT: K 416 MET cc_start: 0.7690 (pmm) cc_final: 0.7446 (pmm) REVERT: K 478 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8632 (mttp) REVERT: K 524 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8536 (p0) REVERT: K 606 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8296 (mm-30) REVERT: L 303 MET cc_start: 0.8079 (tpp) cc_final: 0.7827 (tpp) REVERT: L 416 MET cc_start: 0.7381 (pmm) cc_final: 0.7073 (pmm) REVERT: L 478 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8914 (mttm) REVERT: L 533 GLN cc_start: 0.8865 (mt0) cc_final: 0.8578 (mm-40) REVERT: L 593 ASP cc_start: 0.8649 (t70) cc_final: 0.8227 (t0) REVERT: M 303 MET cc_start: 0.7913 (tpp) cc_final: 0.7148 (tpp) REVERT: M 374 GLN cc_start: 0.6637 (tt0) cc_final: 0.6383 (tm-30) REVERT: M 397 TYR cc_start: 0.8697 (m-80) cc_final: 0.8415 (m-80) REVERT: M 416 MET cc_start: 0.7539 (pmm) cc_final: 0.7316 (pmm) REVERT: M 533 GLN cc_start: 0.8920 (mt0) cc_final: 0.8661 (mp10) REVERT: M 612 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7512 (mm-30) REVERT: M 616 ARG cc_start: 0.7024 (mtt90) cc_final: 0.6769 (mtt90) REVERT: N 118 LEU cc_start: -0.0409 (OUTLIER) cc_final: -0.0618 (mp) REVERT: N 242 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8478 (p0) REVERT: N 303 MET cc_start: 0.7881 (tpp) cc_final: 0.7550 (tpp) REVERT: N 416 MET cc_start: 0.7630 (pmm) cc_final: 0.7407 (pmm) REVERT: N 501 GLU cc_start: 0.8282 (tt0) cc_final: 0.7982 (mt-10) REVERT: N 606 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: O 303 MET cc_start: 0.8301 (tpp) cc_final: 0.7218 (tpp) REVERT: O 368 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8174 (mt-10) REVERT: O 533 GLN cc_start: 0.8958 (mt0) cc_final: 0.8638 (mm110) REVERT: O 593 ASP cc_start: 0.8310 (t70) cc_final: 0.7992 (t0) outliers start: 208 outliers final: 144 residues processed: 835 average time/residue: 0.4930 time to fit residues: 715.2017 Evaluate side-chains 773 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 614 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 424 ASN Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 306 MET Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 588 ASP Chi-restraints excluded: chain J residue 218 ASP Chi-restraints excluded: chain J residue 254 ASP Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 537 LEU Chi-restraints excluded: chain J residue 547 GLU Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 254 ASP Chi-restraints excluded: chain L residue 402 SER Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 535 LEU Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 301 ASP Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 524 ASN Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 242 ASN Chi-restraints excluded: chain N residue 254 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 547 GLU Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain N residue 606 GLU Chi-restraints excluded: chain O residue 218 ASP Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 402 SER Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 536 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 40.0000 chunk 403 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 528 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 606 optimal weight: 0.9980 chunk 491 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 362 optimal weight: 0.7980 chunk 637 optimal weight: 0.0670 chunk 179 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 GLN ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 56910 Z= 0.257 Angle : 0.594 9.271 76950 Z= 0.312 Chirality : 0.048 0.241 9405 Planarity : 0.004 0.056 10020 Dihedral : 5.113 20.264 7860 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.52 % Allowed : 12.13 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -0.37 (0.10), residues: 7290 helix: 1.01 (0.11), residues: 2145 sheet: -0.54 (0.08), residues: 3225 loop : -0.83 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 419 HIS 0.002 0.000 HIS I 635 PHE 0.015 0.001 PHE N 609 TYR 0.009 0.001 TYR E 352 ARG 0.004 0.000 ARG F 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 668 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLN cc_start: 0.7440 (tp-100) cc_final: 0.7182 (tp40) REVERT: A 303 MET cc_start: 0.8032 (tpp) cc_final: 0.7138 (tpp) REVERT: A 407 ILE cc_start: 0.9347 (mm) cc_final: 0.9109 (tp) REVERT: A 543 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8520 (mt-10) REVERT: A 552 VAL cc_start: 0.7304 (OUTLIER) cc_final: 0.7104 (m) REVERT: A 593 ASP cc_start: 0.8360 (t70) cc_final: 0.8115 (t0) REVERT: B 303 MET cc_start: 0.7998 (tpp) cc_final: 0.7372 (tpp) REVERT: B 370 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7784 (mtmm) REVERT: B 533 GLN cc_start: 0.8950 (mt0) cc_final: 0.8711 (mp10) REVERT: B 536 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9041 (p) REVERT: B 543 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8526 (mt-10) REVERT: B 547 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: B 593 ASP cc_start: 0.8429 (t70) cc_final: 0.8164 (t0) REVERT: B 612 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6561 (tm-30) REVERT: C 303 MET cc_start: 0.8013 (tpp) cc_final: 0.6843 (tpp) REVERT: C 407 ILE cc_start: 0.9163 (mm) cc_final: 0.8912 (mt) REVERT: C 416 MET cc_start: 0.7141 (pmm) cc_final: 0.6672 (pmm) REVERT: C 573 GLU cc_start: 0.8062 (tt0) cc_final: 0.7808 (mt-10) REVERT: C 574 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8222 (mtpp) REVERT: C 593 ASP cc_start: 0.8569 (t70) cc_final: 0.8128 (t0) REVERT: D 301 ASP cc_start: 0.8497 (p0) cc_final: 0.8196 (p0) REVERT: D 303 MET cc_start: 0.7996 (tpp) cc_final: 0.7382 (tpp) REVERT: D 323 GLU cc_start: 0.8578 (tt0) cc_final: 0.8358 (pt0) REVERT: D 374 GLN cc_start: 0.6644 (tt0) cc_final: 0.6370 (tm-30) REVERT: D 501 GLU cc_start: 0.8329 (tt0) cc_final: 0.8086 (mt-10) REVERT: D 502 GLN cc_start: 0.8468 (tm130) cc_final: 0.7813 (tp40) REVERT: D 547 GLU cc_start: 0.8148 (tt0) cc_final: 0.7821 (tm-30) REVERT: D 574 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8343 (ttmm) REVERT: E 214 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6908 (tt) REVERT: E 284 MET cc_start: 0.8384 (tpt) cc_final: 0.8140 (tpp) REVERT: E 290 ASP cc_start: 0.8810 (m-30) cc_final: 0.8588 (m-30) REVERT: E 303 MET cc_start: 0.7905 (tpp) cc_final: 0.7233 (tpp) REVERT: E 593 ASP cc_start: 0.8357 (t70) cc_final: 0.7876 (t0) REVERT: F 331 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7940 (tt0) REVERT: F 368 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8113 (mt-10) REVERT: F 397 TYR cc_start: 0.8671 (m-80) cc_final: 0.8325 (m-80) REVERT: F 407 ILE cc_start: 0.9232 (mm) cc_final: 0.8892 (mt) REVERT: F 485 LYS cc_start: 0.8486 (tttm) cc_final: 0.8095 (tptt) REVERT: F 547 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: G 284 MET cc_start: 0.8431 (tpp) cc_final: 0.7982 (mpp) REVERT: G 303 MET cc_start: 0.8013 (tpp) cc_final: 0.7070 (tpp) REVERT: G 543 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8488 (mt-10) REVERT: G 547 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8368 (mm-30) REVERT: G 593 ASP cc_start: 0.8181 (t70) cc_final: 0.7762 (t0) REVERT: G 606 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: H 303 MET cc_start: 0.7927 (tpp) cc_final: 0.6870 (tpp) REVERT: H 363 MET cc_start: 0.8045 (mtm) cc_final: 0.7787 (mtm) REVERT: H 368 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8153 (mt-10) REVERT: H 407 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8940 (tp) REVERT: H 478 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8710 (mttp) REVERT: H 533 GLN cc_start: 0.8951 (mt0) cc_final: 0.8719 (mp10) REVERT: H 616 ARG cc_start: 0.7450 (mtt90) cc_final: 0.6868 (ttm110) REVERT: H 638 GLU cc_start: 0.7889 (tp30) cc_final: 0.7641 (tp30) REVERT: I 300 GLN cc_start: 0.7157 (tp-100) cc_final: 0.6811 (tp40) REVERT: I 368 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7846 (mt-10) REVERT: I 374 GLN cc_start: 0.6341 (tt0) cc_final: 0.6099 (tm-30) REVERT: I 407 ILE cc_start: 0.9296 (mm) cc_final: 0.8887 (tp) REVERT: I 533 GLN cc_start: 0.8997 (mt0) cc_final: 0.8763 (mp10) REVERT: J 284 MET cc_start: 0.8443 (tpp) cc_final: 0.8089 (mpp) REVERT: J 303 MET cc_start: 0.7821 (tpp) cc_final: 0.7243 (tpp) REVERT: J 368 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8222 (mt-10) REVERT: J 543 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8328 (mt-10) REVERT: K 303 MET cc_start: 0.7831 (tpp) cc_final: 0.7508 (tpp) REVERT: K 368 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8070 (mm-30) REVERT: K 374 GLN cc_start: 0.6740 (tt0) cc_final: 0.6351 (tm-30) REVERT: K 416 MET cc_start: 0.7988 (pmm) cc_final: 0.7770 (pmm) REVERT: K 478 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8672 (mttp) REVERT: K 524 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8360 (p0) REVERT: K 606 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8245 (mm-30) REVERT: L 214 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6655 (tt) REVERT: L 284 MET cc_start: 0.8507 (tpp) cc_final: 0.8304 (mpp) REVERT: L 303 MET cc_start: 0.8057 (tpp) cc_final: 0.7821 (tpp) REVERT: L 416 MET cc_start: 0.7412 (pmm) cc_final: 0.6985 (pmm) REVERT: L 447 GLU cc_start: 0.8634 (pt0) cc_final: 0.8273 (pm20) REVERT: L 478 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8911 (mttm) REVERT: L 593 ASP cc_start: 0.8599 (t70) cc_final: 0.8189 (t0) REVERT: M 294 LEU cc_start: 0.8935 (pp) cc_final: 0.8612 (pt) REVERT: M 303 MET cc_start: 0.7849 (tpp) cc_final: 0.7214 (tpp) REVERT: M 337 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8145 (pt) REVERT: M 374 GLN cc_start: 0.6573 (tt0) cc_final: 0.6351 (tm-30) REVERT: M 397 TYR cc_start: 0.8702 (m-80) cc_final: 0.8437 (m-80) REVERT: M 407 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8918 (mt) REVERT: M 424 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8419 (p0) REVERT: M 501 GLU cc_start: 0.8225 (tt0) cc_final: 0.7903 (mt-10) REVERT: M 533 GLN cc_start: 0.8931 (mt0) cc_final: 0.8653 (mp10) REVERT: M 612 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7425 (mm-30) REVERT: N 284 MET cc_start: 0.8556 (tpp) cc_final: 0.8153 (mpp) REVERT: N 303 MET cc_start: 0.7882 (tpp) cc_final: 0.7561 (tpp) REVERT: N 416 MET cc_start: 0.7622 (pmm) cc_final: 0.7376 (pmm) REVERT: N 501 GLU cc_start: 0.8265 (tt0) cc_final: 0.7971 (mt-10) REVERT: N 525 THR cc_start: 0.8774 (t) cc_final: 0.7991 (m) REVERT: N 577 LEU cc_start: 0.8454 (mp) cc_final: 0.8163 (mp) REVERT: N 606 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: O 303 MET cc_start: 0.8227 (tpp) cc_final: 0.7191 (tpp) REVERT: O 368 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8154 (mt-10) REVERT: O 533 GLN cc_start: 0.8959 (mt0) cc_final: 0.8652 (mm110) REVERT: O 593 ASP cc_start: 0.8271 (t70) cc_final: 0.7960 (t0) outliers start: 219 outliers final: 141 residues processed: 851 average time/residue: 0.4893 time to fit residues: 727.6231 Evaluate side-chains 781 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 625 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 606 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 588 ASP Chi-restraints excluded: chain J residue 254 ASP Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 524 ASN Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 537 LEU Chi-restraints excluded: chain J residue 547 GLU Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 402 SER Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 301 ASP Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 424 ASN Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 524 ASN Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain N residue 254 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 297 THR Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 547 GLU Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain N residue 606 GLU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 402 SER Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 456 VAL Chi-restraints excluded: chain O residue 536 VAL Chi-restraints excluded: chain O residue 552 VAL Chi-restraints excluded: chain O residue 616 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 0.7980 chunk 639 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 417 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 711 optimal weight: 10.0000 chunk 590 optimal weight: 6.9990 chunk 329 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 373 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN I 524 ASN ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 300 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 56910 Z= 0.335 Angle : 0.624 9.678 76950 Z= 0.326 Chirality : 0.049 0.183 9405 Planarity : 0.005 0.054 10020 Dihedral : 5.152 21.991 7860 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.43 % Rotamer: Outliers : 3.63 % Allowed : 13.86 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -0.37 (0.10), residues: 7290 helix: 1.29 (0.11), residues: 2055 sheet: -0.61 (0.08), residues: 3330 loop : -0.94 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 419 HIS 0.002 0.001 HIS C 635 PHE 0.019 0.001 PHE F 609 TYR 0.011 0.001 TYR J 600 ARG 0.003 0.000 ARG C 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 621 time to evaluate : 4.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 GLN cc_start: 0.7492 (tp-100) cc_final: 0.7276 (tp40) REVERT: A 303 MET cc_start: 0.8103 (tpp) cc_final: 0.7089 (tpp) REVERT: A 407 ILE cc_start: 0.9388 (mm) cc_final: 0.9110 (tp) REVERT: A 543 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 552 VAL cc_start: 0.7150 (OUTLIER) cc_final: 0.6943 (m) REVERT: A 593 ASP cc_start: 0.8370 (t70) cc_final: 0.8131 (t0) REVERT: B 257 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 303 MET cc_start: 0.8008 (tpp) cc_final: 0.7110 (tpp) REVERT: B 370 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7707 (mtmm) REVERT: B 444 ASP cc_start: 0.8262 (t0) cc_final: 0.8007 (t0) REVERT: B 524 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8545 (p0) REVERT: B 528 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8674 (ttm) REVERT: B 533 GLN cc_start: 0.8985 (mt0) cc_final: 0.8711 (mp10) REVERT: B 536 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9066 (p) REVERT: B 543 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8570 (mt-10) REVERT: B 547 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: B 593 ASP cc_start: 0.8387 (t70) cc_final: 0.7905 (t0) REVERT: C 303 MET cc_start: 0.8076 (tpp) cc_final: 0.6823 (tpp) REVERT: C 407 ILE cc_start: 0.9158 (mm) cc_final: 0.8891 (mt) REVERT: C 416 MET cc_start: 0.7178 (pmm) cc_final: 0.6694 (pmm) REVERT: C 535 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9019 (tt) REVERT: C 573 GLU cc_start: 0.8107 (tt0) cc_final: 0.7849 (mt-10) REVERT: C 574 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8204 (mtpp) REVERT: C 593 ASP cc_start: 0.8515 (t70) cc_final: 0.8237 (t0) REVERT: D 301 ASP cc_start: 0.8521 (p0) cc_final: 0.8106 (p0) REVERT: D 303 MET cc_start: 0.8038 (tpp) cc_final: 0.7359 (tpp) REVERT: D 323 GLU cc_start: 0.8562 (tt0) cc_final: 0.8282 (pt0) REVERT: D 374 GLN cc_start: 0.6634 (tt0) cc_final: 0.6353 (tm-30) REVERT: D 501 GLU cc_start: 0.8363 (tt0) cc_final: 0.8110 (mt-10) REVERT: D 547 GLU cc_start: 0.8217 (tt0) cc_final: 0.7915 (tm-30) REVERT: D 574 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8335 (ttmm) REVERT: D 593 ASP cc_start: 0.8434 (t70) cc_final: 0.8106 (t0) REVERT: E 214 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6798 (tt) REVERT: E 284 MET cc_start: 0.8326 (tpt) cc_final: 0.8060 (tpp) REVERT: E 290 ASP cc_start: 0.8827 (m-30) cc_final: 0.8611 (m-30) REVERT: E 303 MET cc_start: 0.7997 (tpp) cc_final: 0.7275 (tpp) REVERT: E 524 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8767 (p0) REVERT: E 593 ASP cc_start: 0.8375 (t70) cc_final: 0.7928 (t0) REVERT: F 331 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7982 (tt0) REVERT: F 368 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8135 (mt-10) REVERT: F 397 TYR cc_start: 0.8695 (m-80) cc_final: 0.8412 (m-80) REVERT: F 485 LYS cc_start: 0.8486 (tttm) cc_final: 0.8129 (tptt) REVERT: F 547 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: G 284 MET cc_start: 0.8471 (tpp) cc_final: 0.8254 (tpp) REVERT: G 303 MET cc_start: 0.8034 (tpp) cc_final: 0.7038 (tpp) REVERT: G 374 GLN cc_start: 0.5141 (tm-30) cc_final: 0.4651 (tm-30) REVERT: G 543 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8399 (mt-10) REVERT: G 547 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: G 593 ASP cc_start: 0.8202 (t70) cc_final: 0.7789 (t0) REVERT: G 606 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: H 303 MET cc_start: 0.7972 (tpp) cc_final: 0.6882 (tpp) REVERT: H 368 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8158 (mt-10) REVERT: H 407 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8940 (tp) REVERT: H 416 MET cc_start: 0.7356 (pmm) cc_final: 0.7106 (pmm) REVERT: H 478 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8712 (mttp) REVERT: H 533 GLN cc_start: 0.9034 (mt0) cc_final: 0.8774 (mp10) REVERT: H 616 ARG cc_start: 0.7522 (mtt90) cc_final: 0.6997 (ttm110) REVERT: I 300 GLN cc_start: 0.7124 (tp-100) cc_final: 0.6768 (tp40) REVERT: I 368 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7892 (mt-10) REVERT: I 374 GLN cc_start: 0.6345 (tt0) cc_final: 0.6117 (tm-30) REVERT: I 407 ILE cc_start: 0.9301 (mm) cc_final: 0.8917 (tp) REVERT: I 533 GLN cc_start: 0.9073 (mt0) cc_final: 0.8779 (mp10) REVERT: J 214 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6934 (tt) REVERT: J 303 MET cc_start: 0.7918 (tpp) cc_final: 0.7260 (tpp) REVERT: J 368 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8034 (mt-10) REVERT: J 543 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8381 (mt-10) REVERT: K 242 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8755 (p0) REVERT: K 303 MET cc_start: 0.7872 (tpp) cc_final: 0.7286 (tpp) REVERT: K 368 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8096 (mm-30) REVERT: K 416 MET cc_start: 0.7973 (pmm) cc_final: 0.7745 (pmm) REVERT: K 478 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8615 (mttp) REVERT: K 524 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8522 (p0) REVERT: K 606 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8277 (mm-30) REVERT: L 214 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6561 (tt) REVERT: L 242 ASN cc_start: 0.8979 (p0) cc_final: 0.8621 (p0) REVERT: L 284 MET cc_start: 0.8559 (tpp) cc_final: 0.8280 (mpp) REVERT: L 303 MET cc_start: 0.8039 (tpp) cc_final: 0.7804 (tpp) REVERT: L 416 MET cc_start: 0.7542 (pmm) cc_final: 0.7313 (pmm) REVERT: L 478 LYS cc_start: 0.9137 (mtpp) cc_final: 0.8896 (mttm) REVERT: L 593 ASP cc_start: 0.8636 (t70) cc_final: 0.8245 (t0) REVERT: M 285 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8841 (mm) REVERT: M 303 MET cc_start: 0.7951 (tpp) cc_final: 0.7182 (tpp) REVERT: M 374 GLN cc_start: 0.6553 (tt0) cc_final: 0.6309 (tm-30) REVERT: M 397 TYR cc_start: 0.8726 (m-80) cc_final: 0.8483 (m-80) REVERT: M 407 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8948 (mt) REVERT: M 416 MET cc_start: 0.7602 (pmm) cc_final: 0.7255 (pmm) REVERT: M 501 GLU cc_start: 0.8302 (tt0) cc_final: 0.7970 (mt-10) REVERT: M 533 GLN cc_start: 0.8952 (mt0) cc_final: 0.8694 (mp10) REVERT: M 612 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7443 (mm-30) REVERT: N 303 MET cc_start: 0.7877 (tpp) cc_final: 0.7518 (tpp) REVERT: N 416 MET cc_start: 0.7612 (pmm) cc_final: 0.7355 (pmm) REVERT: N 501 GLU cc_start: 0.8281 (tt0) cc_final: 0.7983 (mt-10) REVERT: N 606 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: O 284 MET cc_start: 0.8558 (tpp) cc_final: 0.8239 (mpp) REVERT: O 303 MET cc_start: 0.8296 (tpp) cc_final: 0.7205 (tpp) REVERT: O 368 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8104 (mt-10) REVERT: O 533 GLN cc_start: 0.8964 (mt0) cc_final: 0.8640 (mm110) REVERT: O 593 ASP cc_start: 0.8316 (t70) cc_final: 0.7952 (t0) outliers start: 226 outliers final: 170 residues processed: 812 average time/residue: 0.5366 time to fit residues: 769.3985 Evaluate side-chains 787 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 597 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 606 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 588 ASP Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 254 ASP Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 524 ASN Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 537 LEU Chi-restraints excluded: chain J residue 547 GLU Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 291 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 402 SER Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 301 ASP Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 524 ASN Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain N residue 254 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 295 VAL Chi-restraints excluded: chain N residue 297 THR Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 320 VAL Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 547 GLU Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain N residue 606 GLU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 315 ILE Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain O residue 402 SER Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 456 VAL Chi-restraints excluded: chain O residue 536 VAL Chi-restraints excluded: chain O residue 552 VAL Chi-restraints excluded: chain O residue 616 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 519 optimal weight: 2.9990 chunk 402 optimal weight: 20.0000 chunk 598 optimal weight: 5.9990 chunk 397 optimal weight: 20.0000 chunk 708 optimal weight: 1.9990 chunk 443 optimal weight: 3.9990 chunk 431 optimal weight: 1.9990 chunk 327 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 340 GLN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 635 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 56910 Z= 0.454 Angle : 0.681 11.103 76950 Z= 0.354 Chirality : 0.050 0.195 9405 Planarity : 0.005 0.062 10020 Dihedral : 5.377 23.830 7860 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.88 % Favored : 95.91 % Rotamer: Outliers : 4.05 % Allowed : 14.31 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -0.52 (0.10), residues: 7290 helix: 1.07 (0.11), residues: 2100 sheet: -0.66 (0.08), residues: 3315 loop : -1.04 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 419 HIS 0.003 0.001 HIS F 635 PHE 0.016 0.002 PHE O 580 TYR 0.011 0.002 TYR J 600 ARG 0.005 0.000 ARG E 477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 583 time to evaluate : 4.827 Fit side-chains revert: symmetry clash REVERT: A 300 GLN cc_start: 0.7507 (tp-100) cc_final: 0.7307 (tp40) REVERT: A 303 MET cc_start: 0.8126 (tpp) cc_final: 0.7086 (tpp) REVERT: A 407 ILE cc_start: 0.9399 (mm) cc_final: 0.9123 (tp) REVERT: A 543 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8531 (mt-10) REVERT: A 553 PRO cc_start: 0.6692 (OUTLIER) cc_final: 0.6471 (Cg_endo) REVERT: A 593 ASP cc_start: 0.8339 (t70) cc_final: 0.8040 (t0) REVERT: B 257 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7959 (mm-30) REVERT: B 303 MET cc_start: 0.8025 (tpp) cc_final: 0.7065 (tpp) REVERT: B 337 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 370 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7767 (mtmm) REVERT: B 444 ASP cc_start: 0.8338 (t0) cc_final: 0.8123 (t0) REVERT: B 524 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8595 (p0) REVERT: B 533 GLN cc_start: 0.8993 (mt0) cc_final: 0.8683 (mp10) REVERT: B 536 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9120 (p) REVERT: B 543 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 547 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8463 (mm-30) REVERT: B 593 ASP cc_start: 0.8400 (t70) cc_final: 0.7928 (t0) REVERT: B 612 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6509 (tm-30) REVERT: C 303 MET cc_start: 0.8115 (tpp) cc_final: 0.6823 (tpp) REVERT: C 337 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8210 (pp) REVERT: C 407 ILE cc_start: 0.9160 (mm) cc_final: 0.8907 (mt) REVERT: C 416 MET cc_start: 0.7186 (pmm) cc_final: 0.6674 (pmm) REVERT: C 535 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9022 (tt) REVERT: C 573 GLU cc_start: 0.8143 (tt0) cc_final: 0.7869 (mt-10) REVERT: C 574 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8202 (mtpp) REVERT: C 593 ASP cc_start: 0.8536 (t70) cc_final: 0.8245 (t0) REVERT: D 301 ASP cc_start: 0.8469 (p0) cc_final: 0.8068 (p0) REVERT: D 303 MET cc_start: 0.8007 (tpp) cc_final: 0.7160 (tpp) REVERT: D 374 GLN cc_start: 0.6633 (tt0) cc_final: 0.6353 (tm-30) REVERT: D 416 MET cc_start: 0.7754 (pmm) cc_final: 0.7533 (pmm) REVERT: D 501 GLU cc_start: 0.8437 (tt0) cc_final: 0.8117 (mt-10) REVERT: D 547 GLU cc_start: 0.8274 (tt0) cc_final: 0.7994 (tm-30) REVERT: D 574 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8309 (ttmm) REVERT: D 593 ASP cc_start: 0.8436 (t70) cc_final: 0.8092 (t0) REVERT: E 214 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6697 (tt) REVERT: E 284 MET cc_start: 0.8210 (tpt) cc_final: 0.7968 (tpp) REVERT: E 290 ASP cc_start: 0.8866 (m-30) cc_final: 0.8658 (m-30) REVERT: E 303 MET cc_start: 0.8039 (tpp) cc_final: 0.7291 (tpp) REVERT: E 524 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8828 (p0) REVERT: E 593 ASP cc_start: 0.8585 (t70) cc_final: 0.8085 (t0) REVERT: F 303 MET cc_start: 0.7950 (tpp) cc_final: 0.7239 (tpp) REVERT: F 368 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8134 (mt-10) REVERT: F 397 TYR cc_start: 0.8716 (m-80) cc_final: 0.8433 (m-80) REVERT: F 407 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9017 (mt) REVERT: F 547 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: G 284 MET cc_start: 0.8500 (tpp) cc_final: 0.8290 (tpp) REVERT: G 303 MET cc_start: 0.7931 (tpp) cc_final: 0.6936 (tpp) REVERT: G 394 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7819 (mmmt) REVERT: G 447 GLU cc_start: 0.8923 (pt0) cc_final: 0.8234 (pm20) REVERT: G 543 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8394 (mt-10) REVERT: G 547 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (mm-30) REVERT: G 593 ASP cc_start: 0.8222 (t70) cc_final: 0.7810 (t0) REVERT: G 606 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: H 300 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6642 (tp40) REVERT: H 368 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8124 (mt-10) REVERT: H 407 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8950 (tp) REVERT: H 416 MET cc_start: 0.7332 (pmm) cc_final: 0.7081 (pmm) REVERT: H 478 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8605 (mttp) REVERT: H 533 GLN cc_start: 0.9075 (mt0) cc_final: 0.8874 (mm-40) REVERT: H 616 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7141 (ttm110) REVERT: I 290 ASP cc_start: 0.8867 (m-30) cc_final: 0.8592 (m-30) REVERT: I 300 GLN cc_start: 0.7138 (tp-100) cc_final: 0.6791 (tp40) REVERT: I 368 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7919 (mt-10) REVERT: I 374 GLN cc_start: 0.6339 (tt0) cc_final: 0.6034 (tm-30) REVERT: I 407 ILE cc_start: 0.9322 (mm) cc_final: 0.8962 (tp) REVERT: I 533 GLN cc_start: 0.9104 (mt0) cc_final: 0.8786 (mp10) REVERT: J 284 MET cc_start: 0.8429 (tpp) cc_final: 0.8068 (mpp) REVERT: J 303 MET cc_start: 0.7941 (tpp) cc_final: 0.7242 (tpp) REVERT: J 368 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7972 (mt-10) REVERT: J 374 GLN cc_start: 0.4771 (tm-30) cc_final: 0.4444 (tm-30) REVERT: J 543 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8528 (mt-10) REVERT: K 303 MET cc_start: 0.7899 (tpp) cc_final: 0.7263 (tpp) REVERT: K 368 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8090 (mm-30) REVERT: K 374 GLN cc_start: 0.6747 (tt0) cc_final: 0.6324 (tm-30) REVERT: K 416 MET cc_start: 0.7845 (pmm) cc_final: 0.7556 (pmm) REVERT: K 478 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8619 (mttp) REVERT: K 524 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8697 (p0) REVERT: K 593 ASP cc_start: 0.8440 (t70) cc_final: 0.8086 (t0) REVERT: K 606 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8351 (mm-30) REVERT: L 303 MET cc_start: 0.7976 (tpp) cc_final: 0.7699 (tpp) REVERT: L 478 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8856 (mttm) REVERT: L 593 ASP cc_start: 0.8653 (t70) cc_final: 0.8253 (t0) REVERT: M 303 MET cc_start: 0.7970 (tpp) cc_final: 0.7176 (tpp) REVERT: M 374 GLN cc_start: 0.6382 (tt0) cc_final: 0.6129 (tm-30) REVERT: M 407 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8970 (mt) REVERT: M 416 MET cc_start: 0.7577 (pmm) cc_final: 0.7182 (pmm) REVERT: M 424 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8230 (p0) REVERT: M 501 GLU cc_start: 0.8337 (tt0) cc_final: 0.7967 (mt-10) REVERT: M 533 GLN cc_start: 0.8957 (mt0) cc_final: 0.8676 (mp10) REVERT: M 612 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7504 (mm-30) REVERT: N 284 MET cc_start: 0.8621 (tpp) cc_final: 0.8249 (mpp) REVERT: N 303 MET cc_start: 0.7874 (tpp) cc_final: 0.7450 (tpp) REVERT: N 416 MET cc_start: 0.7683 (pmm) cc_final: 0.7481 (pmm) REVERT: N 501 GLU cc_start: 0.8331 (tt0) cc_final: 0.7944 (mt-10) REVERT: N 606 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: O 214 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6625 (tt) REVERT: O 303 MET cc_start: 0.8189 (tpp) cc_final: 0.7076 (tpp) REVERT: O 368 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8113 (mt-10) REVERT: O 533 GLN cc_start: 0.9023 (mt0) cc_final: 0.8634 (mm110) REVERT: O 553 PRO cc_start: 0.6990 (OUTLIER) cc_final: 0.6770 (Cg_endo) REVERT: O 593 ASP cc_start: 0.8422 (t70) cc_final: 0.8063 (t0) outliers start: 252 outliers final: 191 residues processed: 803 average time/residue: 0.4802 time to fit residues: 676.6498 Evaluate side-chains 772 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 559 time to evaluate : 4.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 PRO Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 553 PRO Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 394 LYS Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 606 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 588 ASP Chi-restraints excluded: chain J residue 254 ASP Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 320 VAL Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 524 ASN Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 537 LEU Chi-restraints excluded: chain J residue 547 GLU Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 291 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain K residue 553 PRO Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 337 LEU Chi-restraints excluded: chain L residue 402 SER Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 301 ASP Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 424 ASN Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain M residue 603 ILE Chi-restraints excluded: chain N residue 254 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 295 VAL Chi-restraints excluded: chain N residue 297 THR Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 320 VAL Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 535 LEU Chi-restraints excluded: chain N residue 547 GLU Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain N residue 606 GLU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 291 THR Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain O residue 402 SER Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 456 VAL Chi-restraints excluded: chain O residue 536 VAL Chi-restraints excluded: chain O residue 552 VAL Chi-restraints excluded: chain O residue 553 PRO Chi-restraints excluded: chain O residue 603 ILE Chi-restraints excluded: chain O residue 616 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 423 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 450 optimal weight: 4.9990 chunk 482 optimal weight: 0.6980 chunk 350 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 556 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 524 ASN ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 56910 Z= 0.242 Angle : 0.591 10.359 76950 Z= 0.308 Chirality : 0.048 0.158 9405 Planarity : 0.004 0.055 10020 Dihedral : 4.981 20.623 7860 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.42 % Favored : 96.38 % Rotamer: Outliers : 3.61 % Allowed : 14.97 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -0.28 (0.10), residues: 7290 helix: 1.36 (0.11), residues: 2100 sheet: -0.60 (0.08), residues: 3330 loop : -0.87 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 419 HIS 0.002 0.000 HIS C 635 PHE 0.013 0.001 PHE O 580 TYR 0.009 0.001 TYR E 352 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 636 time to evaluate : 4.896 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.8041 (tpp) cc_final: 0.6991 (tpp) REVERT: A 337 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7935 (pp) REVERT: A 407 ILE cc_start: 0.9389 (mm) cc_final: 0.9080 (tp) REVERT: A 543 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 593 ASP cc_start: 0.8332 (t70) cc_final: 0.8070 (t0) REVERT: B 257 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7850 (mm-30) REVERT: B 303 MET cc_start: 0.7939 (tpp) cc_final: 0.7231 (tpp) REVERT: B 337 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8092 (pp) REVERT: B 370 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7700 (mtmm) REVERT: B 444 ASP cc_start: 0.8176 (t0) cc_final: 0.7975 (t0) REVERT: B 524 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8370 (p0) REVERT: B 533 GLN cc_start: 0.8978 (mt0) cc_final: 0.8682 (mp10) REVERT: B 536 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9117 (p) REVERT: B 543 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8582 (mt-10) REVERT: B 547 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8365 (mm-30) REVERT: B 593 ASP cc_start: 0.8430 (t70) cc_final: 0.7953 (t0) REVERT: B 612 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6483 (tm-30) REVERT: C 284 MET cc_start: 0.8654 (tpp) cc_final: 0.8316 (mpp) REVERT: C 303 MET cc_start: 0.7992 (tpp) cc_final: 0.6821 (tpp) REVERT: C 337 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7950 (pp) REVERT: C 407 ILE cc_start: 0.9146 (mm) cc_final: 0.8892 (mt) REVERT: C 416 MET cc_start: 0.7253 (pmm) cc_final: 0.6803 (pmm) REVERT: C 573 GLU cc_start: 0.8078 (tt0) cc_final: 0.7827 (mt-10) REVERT: C 574 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8218 (mtpp) REVERT: C 593 ASP cc_start: 0.8497 (t70) cc_final: 0.8210 (t0) REVERT: D 301 ASP cc_start: 0.8460 (p0) cc_final: 0.8025 (p0) REVERT: D 303 MET cc_start: 0.7945 (tpp) cc_final: 0.7427 (tpp) REVERT: D 374 GLN cc_start: 0.6684 (tt0) cc_final: 0.6411 (tm-30) REVERT: D 501 GLU cc_start: 0.8330 (tt0) cc_final: 0.8096 (mt-10) REVERT: D 547 GLU cc_start: 0.8148 (tt0) cc_final: 0.7833 (tm-30) REVERT: D 574 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8329 (ttmm) REVERT: E 284 MET cc_start: 0.8369 (tpt) cc_final: 0.8120 (tpp) REVERT: E 290 ASP cc_start: 0.8812 (m-30) cc_final: 0.8595 (m-30) REVERT: E 303 MET cc_start: 0.7939 (tpp) cc_final: 0.7249 (tpp) REVERT: E 593 ASP cc_start: 0.8444 (t70) cc_final: 0.7942 (t0) REVERT: F 242 ASN cc_start: 0.8937 (p0) cc_final: 0.8599 (p0) REVERT: F 303 MET cc_start: 0.7939 (tpp) cc_final: 0.7220 (tpp) REVERT: F 331 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7725 (tt0) REVERT: F 368 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8129 (mt-10) REVERT: F 397 TYR cc_start: 0.8676 (m-80) cc_final: 0.8389 (m-80) REVERT: F 485 LYS cc_start: 0.8496 (tttm) cc_final: 0.8119 (tptt) REVERT: F 547 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: G 303 MET cc_start: 0.8021 (tpp) cc_final: 0.7059 (tpp) REVERT: G 374 GLN cc_start: 0.4921 (tm-30) cc_final: 0.4635 (tm-30) REVERT: G 543 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8399 (mt-10) REVERT: G 547 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: G 593 ASP cc_start: 0.8185 (t70) cc_final: 0.7762 (t0) REVERT: G 606 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: G 609 PHE cc_start: 0.7364 (t80) cc_final: 0.7152 (t80) REVERT: H 303 MET cc_start: 0.7832 (tpp) cc_final: 0.6856 (tpp) REVERT: H 368 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8129 (mt-10) REVERT: H 407 ILE cc_start: 0.9233 (mm) cc_final: 0.9017 (tp) REVERT: H 416 MET cc_start: 0.7372 (pmm) cc_final: 0.7155 (pmm) REVERT: H 478 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8748 (mttp) REVERT: H 501 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7960 (mp0) REVERT: H 533 GLN cc_start: 0.9138 (mt0) cc_final: 0.8877 (mm-40) REVERT: H 616 ARG cc_start: 0.7553 (mtt90) cc_final: 0.7050 (ttm110) REVERT: I 290 ASP cc_start: 0.8832 (m-30) cc_final: 0.8574 (m-30) REVERT: I 300 GLN cc_start: 0.7130 (tp-100) cc_final: 0.6796 (tp40) REVERT: I 368 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7942 (mt-10) REVERT: I 374 GLN cc_start: 0.6251 (tt0) cc_final: 0.6030 (tm-30) REVERT: I 397 TYR cc_start: 0.8229 (m-80) cc_final: 0.7744 (m-80) REVERT: I 407 ILE cc_start: 0.9299 (mm) cc_final: 0.8948 (tp) REVERT: I 606 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: J 284 MET cc_start: 0.8454 (tpp) cc_final: 0.8090 (mpp) REVERT: J 303 MET cc_start: 0.7808 (tpp) cc_final: 0.7213 (tpp) REVERT: J 368 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8240 (mt-10) REVERT: J 524 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8711 (p0) REVERT: J 543 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8341 (mt-10) REVERT: J 598 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7508 (ptp90) REVERT: K 303 MET cc_start: 0.7796 (tpp) cc_final: 0.7332 (tpp) REVERT: K 368 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8083 (mm-30) REVERT: K 416 MET cc_start: 0.8015 (pmm) cc_final: 0.7772 (pmm) REVERT: K 478 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8628 (mttp) REVERT: K 524 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8450 (p0) REVERT: K 606 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8251 (mm-30) REVERT: L 284 MET cc_start: 0.8530 (tpp) cc_final: 0.8245 (mpp) REVERT: L 303 MET cc_start: 0.8035 (tpp) cc_final: 0.7729 (tpp) REVERT: L 416 MET cc_start: 0.7624 (pmm) cc_final: 0.7266 (pmm) REVERT: L 478 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8846 (mttm) REVERT: L 593 ASP cc_start: 0.8607 (t70) cc_final: 0.8173 (t0) REVERT: M 303 MET cc_start: 0.7750 (tpp) cc_final: 0.6869 (tpp) REVERT: M 374 GLN cc_start: 0.6624 (tt0) cc_final: 0.6386 (tm-30) REVERT: M 416 MET cc_start: 0.7647 (pmm) cc_final: 0.7229 (pmm) REVERT: M 424 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8133 (p0) REVERT: M 501 GLU cc_start: 0.8223 (tt0) cc_final: 0.8008 (mp0) REVERT: M 612 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7466 (mm-30) REVERT: N 284 MET cc_start: 0.8586 (tpp) cc_final: 0.8089 (mpp) REVERT: N 303 MET cc_start: 0.7934 (tpp) cc_final: 0.7633 (tpp) REVERT: N 416 MET cc_start: 0.7671 (pmm) cc_final: 0.7454 (pmm) REVERT: N 501 GLU cc_start: 0.8311 (tt0) cc_final: 0.7949 (mt-10) REVERT: N 577 LEU cc_start: 0.8397 (mp) cc_final: 0.8173 (mp) REVERT: N 606 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: O 214 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6652 (tt) REVERT: O 284 MET cc_start: 0.8502 (tpp) cc_final: 0.8283 (tpp) REVERT: O 303 MET cc_start: 0.8280 (tpp) cc_final: 0.7169 (tpp) REVERT: O 368 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8128 (mt-10) REVERT: O 533 GLN cc_start: 0.8985 (mt0) cc_final: 0.8702 (mm110) REVERT: O 593 ASP cc_start: 0.8166 (t70) cc_final: 0.7882 (t0) outliers start: 225 outliers final: 164 residues processed: 827 average time/residue: 0.4838 time to fit residues: 704.3451 Evaluate side-chains 785 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 604 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 606 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 390 THR Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 588 ASP Chi-restraints excluded: chain I residue 606 GLU Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 254 ASP Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 524 ASN Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 537 LEU Chi-restraints excluded: chain J residue 598 ARG Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 291 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 394 LYS Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 424 ASN Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 524 ASN Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 536 VAL Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain N residue 254 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 295 VAL Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 320 VAL Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 547 GLU Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain N residue 606 GLU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 291 THR Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 456 VAL Chi-restraints excluded: chain O residue 536 VAL Chi-restraints excluded: chain O residue 552 VAL Chi-restraints excluded: chain O residue 616 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 0.0870 chunk 678 optimal weight: 0.0570 chunk 619 optimal weight: 0.4980 chunk 660 optimal weight: 1.9990 chunk 397 optimal weight: 20.0000 chunk 287 optimal weight: 3.9990 chunk 518 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 chunk 624 optimal weight: 0.8980 chunk 657 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 524 ASN ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 56910 Z= 0.220 Angle : 0.580 12.578 76950 Z= 0.302 Chirality : 0.047 0.190 9405 Planarity : 0.004 0.054 10020 Dihedral : 4.841 19.641 7860 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.52 % Rotamer: Outliers : 3.23 % Allowed : 15.58 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: -0.14 (0.10), residues: 7290 helix: 1.52 (0.11), residues: 2100 sheet: -0.52 (0.09), residues: 3330 loop : -0.85 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 419 HIS 0.002 0.000 HIS C 635 PHE 0.019 0.001 PHE I 609 TYR 0.012 0.001 TYR A 352 ARG 0.006 0.000 ARG M 521 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 640 time to evaluate : 4.817 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.7826 (tpp) cc_final: 0.6883 (tpp) REVERT: A 407 ILE cc_start: 0.9375 (mm) cc_final: 0.9082 (tp) REVERT: A 543 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8443 (mt-10) REVERT: A 593 ASP cc_start: 0.8328 (t70) cc_final: 0.8098 (t0) REVERT: B 257 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 303 MET cc_start: 0.7889 (tpp) cc_final: 0.7240 (tpp) REVERT: B 370 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7692 (mtmt) REVERT: B 533 GLN cc_start: 0.8976 (mt0) cc_final: 0.8670 (mp10) REVERT: B 536 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9103 (p) REVERT: B 547 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: B 593 ASP cc_start: 0.8424 (t70) cc_final: 0.7956 (t0) REVERT: B 612 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6523 (tm-30) REVERT: C 284 MET cc_start: 0.8557 (tpp) cc_final: 0.8315 (mpp) REVERT: C 303 MET cc_start: 0.7986 (tpp) cc_final: 0.6802 (tpp) REVERT: C 337 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7868 (pp) REVERT: C 407 ILE cc_start: 0.9129 (mm) cc_final: 0.8866 (mt) REVERT: C 416 MET cc_start: 0.7551 (pmm) cc_final: 0.7280 (pmm) REVERT: C 573 GLU cc_start: 0.8061 (tt0) cc_final: 0.7821 (mt-10) REVERT: C 574 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8199 (mtpp) REVERT: C 593 ASP cc_start: 0.8561 (t70) cc_final: 0.8271 (t0) REVERT: D 303 MET cc_start: 0.7894 (tpp) cc_final: 0.7437 (tpp) REVERT: D 374 GLN cc_start: 0.6644 (tt0) cc_final: 0.6361 (tm-30) REVERT: D 397 TYR cc_start: 0.8681 (m-80) cc_final: 0.8444 (m-80) REVERT: D 501 GLU cc_start: 0.8299 (tt0) cc_final: 0.8063 (mt-10) REVERT: D 547 GLU cc_start: 0.8137 (tt0) cc_final: 0.7801 (tm-30) REVERT: D 574 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8396 (mtpp) REVERT: E 214 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6857 (tt) REVERT: E 284 MET cc_start: 0.8362 (tpt) cc_final: 0.8110 (tpp) REVERT: E 290 ASP cc_start: 0.8793 (m-30) cc_final: 0.8574 (m-30) REVERT: E 303 MET cc_start: 0.7943 (tpp) cc_final: 0.7270 (tpp) REVERT: E 495 SER cc_start: 0.9484 (p) cc_final: 0.9180 (t) REVERT: E 593 ASP cc_start: 0.8606 (t70) cc_final: 0.8103 (t0) REVERT: F 242 ASN cc_start: 0.8942 (p0) cc_final: 0.8596 (p0) REVERT: F 303 MET cc_start: 0.7913 (tpp) cc_final: 0.7188 (tpp) REVERT: F 331 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7735 (tt0) REVERT: F 368 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8124 (mt-10) REVERT: F 397 TYR cc_start: 0.8667 (m-80) cc_final: 0.8398 (m-80) REVERT: F 485 LYS cc_start: 0.8489 (tttm) cc_final: 0.8108 (tptt) REVERT: F 547 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: G 284 MET cc_start: 0.8623 (tpp) cc_final: 0.8022 (mpp) REVERT: G 303 MET cc_start: 0.7971 (tpp) cc_final: 0.6962 (tpp) REVERT: G 374 GLN cc_start: 0.4891 (tm-30) cc_final: 0.4554 (tm-30) REVERT: G 394 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7809 (mmmt) REVERT: G 424 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7850 (p0) REVERT: G 447 GLU cc_start: 0.8794 (pt0) cc_final: 0.8389 (pm20) REVERT: G 543 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8498 (mt-10) REVERT: G 547 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: G 593 ASP cc_start: 0.8186 (t70) cc_final: 0.7760 (t0) REVERT: G 606 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: H 303 MET cc_start: 0.7838 (tpp) cc_final: 0.6859 (tpp) REVERT: H 368 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8132 (mt-10) REVERT: H 407 ILE cc_start: 0.9260 (mm) cc_final: 0.9025 (tp) REVERT: H 533 GLN cc_start: 0.9147 (mt0) cc_final: 0.8922 (mp10) REVERT: H 616 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7021 (ttm110) REVERT: I 300 GLN cc_start: 0.7110 (tp-100) cc_final: 0.6787 (tp40) REVERT: I 368 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7873 (mt-10) REVERT: I 397 TYR cc_start: 0.8245 (m-80) cc_final: 0.7762 (m-80) REVERT: J 303 MET cc_start: 0.7772 (tpp) cc_final: 0.7229 (tpp) REVERT: J 368 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8235 (mt-10) REVERT: J 374 GLN cc_start: 0.4686 (tm-30) cc_final: 0.4364 (tm-30) REVERT: J 598 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7688 (ttp80) REVERT: K 303 MET cc_start: 0.7797 (tpp) cc_final: 0.7303 (tpp) REVERT: K 416 MET cc_start: 0.7988 (pmm) cc_final: 0.7740 (pmm) REVERT: K 478 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8637 (mttp) REVERT: K 524 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8436 (p0) REVERT: L 284 MET cc_start: 0.8487 (tpp) cc_final: 0.8155 (mpp) REVERT: L 303 MET cc_start: 0.8048 (tpp) cc_final: 0.7765 (tpp) REVERT: L 416 MET cc_start: 0.7648 (pmm) cc_final: 0.7292 (pmm) REVERT: L 478 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8868 (mttm) REVERT: L 593 ASP cc_start: 0.8596 (t70) cc_final: 0.8170 (t0) REVERT: M 303 MET cc_start: 0.7803 (tpp) cc_final: 0.7079 (tpp) REVERT: M 374 GLN cc_start: 0.6645 (tt0) cc_final: 0.6443 (tm-30) REVERT: M 416 MET cc_start: 0.7819 (pmm) cc_final: 0.7408 (pmm) REVERT: M 424 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8120 (p0) REVERT: M 501 GLU cc_start: 0.8246 (tt0) cc_final: 0.7944 (mt-10) REVERT: M 612 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7467 (mm-30) REVERT: N 303 MET cc_start: 0.7951 (tpp) cc_final: 0.7670 (tpp) REVERT: N 416 MET cc_start: 0.7713 (pmm) cc_final: 0.7445 (pmm) REVERT: N 501 GLU cc_start: 0.8264 (tt0) cc_final: 0.7865 (mt-10) REVERT: N 525 THR cc_start: 0.8716 (t) cc_final: 0.7912 (m) REVERT: N 577 LEU cc_start: 0.8458 (mp) cc_final: 0.8250 (mp) REVERT: N 606 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: O 214 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6671 (tt) REVERT: O 284 MET cc_start: 0.8514 (tpp) cc_final: 0.8295 (tpp) REVERT: O 303 MET cc_start: 0.8265 (tpp) cc_final: 0.7141 (tpp) REVERT: O 368 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8145 (mt-10) REVERT: O 593 ASP cc_start: 0.8181 (t70) cc_final: 0.7886 (t0) outliers start: 201 outliers final: 159 residues processed: 810 average time/residue: 0.4936 time to fit residues: 703.8511 Evaluate side-chains 773 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 599 time to evaluate : 5.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 424 ASN Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 394 LYS Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 424 ASN Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 606 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 424 ASN Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 390 THR Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain I residue 588 ASP Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 254 ASP Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 598 ARG Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 291 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 402 SER Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 424 ASN Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain M residue 588 ASP Chi-restraints excluded: chain N residue 254 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 295 VAL Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 402 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 547 GLU Chi-restraints excluded: chain N residue 552 VAL Chi-restraints excluded: chain N residue 606 GLU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 291 THR Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 456 VAL Chi-restraints excluded: chain O residue 536 VAL Chi-restraints excluded: chain O residue 552 VAL Chi-restraints excluded: chain O residue 616 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 0.2980 chunk 698 optimal weight: 8.9990 chunk 426 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 485 optimal weight: 0.8980 chunk 732 optimal weight: 0.0030 chunk 673 optimal weight: 0.7980 chunk 583 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 450 optimal weight: 9.9990 chunk 357 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 56910 Z= 0.196 Angle : 0.571 12.679 76950 Z= 0.297 Chirality : 0.047 0.175 9405 Planarity : 0.004 0.054 10020 Dihedral : 4.688 19.151 7860 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.43 % Rotamer: Outliers : 3.00 % Allowed : 16.14 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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: 0.03 (0.10), residues: 7290 helix: 1.66 (0.11), residues: 2100 sheet: -0.37 (0.09), residues: 3240 loop : -0.87 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 419 HIS 0.002 0.000 HIS A 635 PHE 0.016 0.001 PHE G 609 TYR 0.011 0.001 TYR A 352 ARG 0.004 0.000 ARG M 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 651 time to evaluate : 4.872 Fit side-chains REVERT: A 303 MET cc_start: 0.7781 (tpp) cc_final: 0.6910 (tpp) REVERT: A 337 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 407 ILE cc_start: 0.9396 (mm) cc_final: 0.9076 (tp) REVERT: A 543 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8446 (mt-10) REVERT: B 303 MET cc_start: 0.7832 (tpp) cc_final: 0.7217 (tpp) REVERT: B 370 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7695 (mtmt) REVERT: B 528 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8581 (ttm) REVERT: B 531 ASP cc_start: 0.8516 (t70) cc_final: 0.8133 (t0) REVERT: B 533 GLN cc_start: 0.8980 (mt0) cc_final: 0.8720 (mp10) REVERT: B 536 VAL cc_start: 0.9339 (OUTLIER) cc_final: 0.9087 (p) REVERT: B 547 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: B 593 ASP cc_start: 0.8427 (t70) cc_final: 0.7966 (t0) REVERT: B 612 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6672 (tm-30) REVERT: C 303 MET cc_start: 0.7999 (tpp) cc_final: 0.6773 (tpp) REVERT: C 337 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7936 (pp) REVERT: C 407 ILE cc_start: 0.9115 (mm) cc_final: 0.8840 (mt) REVERT: C 416 MET cc_start: 0.7654 (pmm) cc_final: 0.7410 (pmm) REVERT: C 495 SER cc_start: 0.9411 (p) cc_final: 0.8952 (m) REVERT: C 573 GLU cc_start: 0.8062 (tt0) cc_final: 0.7845 (mt-10) REVERT: C 574 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8209 (mtpp) REVERT: C 593 ASP cc_start: 0.8547 (t70) cc_final: 0.8146 (t0) REVERT: D 303 MET cc_start: 0.7836 (tpp) cc_final: 0.7469 (tpp) REVERT: D 374 GLN cc_start: 0.6662 (tt0) cc_final: 0.6373 (tm-30) REVERT: D 397 TYR cc_start: 0.8691 (m-80) cc_final: 0.8457 (m-80) REVERT: D 547 GLU cc_start: 0.8100 (tt0) cc_final: 0.7763 (tm-30) REVERT: D 574 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8380 (mtpp) REVERT: E 214 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6794 (tt) REVERT: E 284 MET cc_start: 0.8356 (tpt) cc_final: 0.8075 (tpp) REVERT: E 303 MET cc_start: 0.7970 (tpp) cc_final: 0.7328 (tpp) REVERT: E 495 SER cc_start: 0.9383 (p) cc_final: 0.9102 (t) REVERT: E 593 ASP cc_start: 0.8426 (t70) cc_final: 0.8156 (t0) REVERT: F 242 ASN cc_start: 0.8933 (p0) cc_final: 0.8667 (p0) REVERT: F 331 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7721 (tt0) REVERT: F 368 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8086 (mt-10) REVERT: F 397 TYR cc_start: 0.8647 (m-80) cc_final: 0.8413 (m-80) REVERT: F 485 LYS cc_start: 0.8492 (tttm) cc_final: 0.8107 (tptt) REVERT: F 547 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: G 242 ASN cc_start: 0.8815 (p0) cc_final: 0.8573 (p0) REVERT: G 284 MET cc_start: 0.8540 (tpp) cc_final: 0.7852 (mpp) REVERT: G 303 MET cc_start: 0.8048 (tpp) cc_final: 0.7015 (tpp) REVERT: G 374 GLN cc_start: 0.4964 (tm-30) cc_final: 0.4642 (tm-30) REVERT: G 394 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7798 (mmmt) REVERT: G 416 MET cc_start: 0.7714 (pmm) cc_final: 0.7490 (pmm) REVERT: G 424 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7932 (p0) REVERT: G 543 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8496 (mt-10) REVERT: G 547 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: G 593 ASP cc_start: 0.8186 (t70) cc_final: 0.7758 (t0) REVERT: G 606 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: H 303 MET cc_start: 0.7944 (tpp) cc_final: 0.6912 (tpp) REVERT: H 368 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8111 (mt-10) REVERT: H 407 ILE cc_start: 0.9268 (mm) cc_final: 0.9036 (tp) REVERT: H 533 GLN cc_start: 0.9133 (mt0) cc_final: 0.8924 (mp10) REVERT: H 616 ARG cc_start: 0.7556 (mtt90) cc_final: 0.6917 (ttm110) REVERT: I 300 GLN cc_start: 0.7349 (tp-100) cc_final: 0.7011 (tp40) REVERT: I 368 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7870 (mt-10) REVERT: I 374 GLN cc_start: 0.5159 (tm-30) cc_final: 0.4885 (tm-30) REVERT: I 397 TYR cc_start: 0.8164 (m-80) cc_final: 0.7710 (m-80) REVERT: I 407 ILE cc_start: 0.9304 (mm) cc_final: 0.8973 (tp) REVERT: J 284 MET cc_start: 0.8488 (tpp) cc_final: 0.8062 (mpp) REVERT: J 303 MET cc_start: 0.7818 (tpp) cc_final: 0.7328 (tpp) REVERT: J 374 GLN cc_start: 0.4593 (tm-30) cc_final: 0.4352 (tm-30) REVERT: J 598 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7537 (ptp90) REVERT: K 303 MET cc_start: 0.7819 (tpp) cc_final: 0.7382 (tpp) REVERT: K 368 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7935 (mm-30) REVERT: K 478 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8678 (mttp) REVERT: K 524 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8389 (p0) REVERT: L 284 MET cc_start: 0.8458 (tpp) cc_final: 0.8136 (mpp) REVERT: L 303 MET cc_start: 0.8027 (tpp) cc_final: 0.7726 (tpp) REVERT: L 478 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8894 (mttm) REVERT: L 593 ASP cc_start: 0.8591 (t70) cc_final: 0.8168 (t0) REVERT: M 303 MET cc_start: 0.7758 (tpp) cc_final: 0.7054 (tpp) REVERT: M 337 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8079 (pt) REVERT: M 416 MET cc_start: 0.7799 (pmm) cc_final: 0.7433 (pmm) REVERT: M 424 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8112 (p0) REVERT: M 501 GLU cc_start: 0.8206 (tt0) cc_final: 0.7931 (mt-10) REVERT: M 612 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7494 (mm-30) REVERT: N 284 MET cc_start: 0.8496 (tpp) cc_final: 0.8203 (mpp) REVERT: N 303 MET cc_start: 0.7939 (tpp) cc_final: 0.7599 (tpp) REVERT: N 416 MET cc_start: 0.7826 (pmm) cc_final: 0.7540 (pmm) REVERT: N 501 GLU cc_start: 0.8201 (tt0) cc_final: 0.7854 (mt-10) REVERT: N 525 THR cc_start: 0.8646 (t) cc_final: 0.7749 (m) REVERT: N 606 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: O 214 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6650 (tt) REVERT: O 284 MET cc_start: 0.8519 (tpp) cc_final: 0.8288 (tpp) REVERT: O 303 MET cc_start: 0.8226 (tpp) cc_final: 0.7101 (tpp) REVERT: O 368 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8125 (mt-10) REVERT: O 593 ASP cc_start: 0.8159 (t70) cc_final: 0.7865 (t0) outliers start: 187 outliers final: 151 residues processed: 810 average time/residue: 0.4795 time to fit residues: 680.7538 Evaluate side-chains 776 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 607 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 524 ASN Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 524 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 424 ASN Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 451 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ASN Chi-restraints excluded: chain E residue 535 LEU Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 451 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 547 GLU Chi-restraints excluded: chain F residue 588 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 254 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 394 LYS Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 424 ASN Chi-restraints excluded: chain G residue 439 SER Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 547 GLU Chi-restraints excluded: chain G residue 606 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 373 THR Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 424 ASN Chi-restraints excluded: chain H residue 439 SER Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 390 THR Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 439 SER Chi-restraints excluded: chain I residue 451 ILE Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 552 VAL Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 390 THR Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 451 ILE Chi-restraints excluded: chain J residue 456 VAL Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 598 ARG Chi-restraints excluded: chain K residue 244 VAL Chi-restraints excluded: chain K residue 254 ASP Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 291 THR Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 402 SER Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain K residue 451 ILE Chi-restraints excluded: chain K residue 524 ASN Chi-restraints excluded: chain K residue 537 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 394 LYS Chi-restraints excluded: chain L residue 439 SER Chi-restraints excluded: chain L residue 451 ILE Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 588 ASP Chi-restraints excluded: chain M residue 291 THR Chi-restraints excluded: chain M residue 337 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 424 ASN Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 451 ILE Chi-restraints excluded: chain M residue 514 VAL Chi-restraints excluded: chain M residue 528 MET Chi-restraints excluded: chain M residue 552 VAL Chi-restraints excluded: chain N residue 254 ASP Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 295 VAL Chi-restraints excluded: chain N residue 301 ASP Chi-restraints excluded: chain N residue 306 MET Chi-restraints excluded: chain N residue 320 VAL Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 524 ASN Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 547 GLU Chi-restraints excluded: chain N residue 606 GLU Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 291 THR Chi-restraints excluded: chain O residue 301 ASP Chi-restraints excluded: chain O residue 394 LYS Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 451 ILE Chi-restraints excluded: chain O residue 456 VAL Chi-restraints excluded: chain O residue 536 VAL Chi-restraints excluded: chain O residue 552 VAL Chi-restraints excluded: chain O residue 616 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 1.9990 chunk 621 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 537 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 584 optimal weight: 0.5980 chunk 244 optimal weight: 9.9990 chunk 599 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118587 restraints weight = 57859.351| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.11 r_work: 0.3086 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 56910 Z= 0.296 Angle : 0.609 12.286 76950 Z= 0.316 Chirality : 0.048 0.275 9405 Planarity : 0.005 0.052 10020 Dihedral : 4.863 19.686 7860 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.24 % Favored : 96.57 % Rotamer: Outliers : 3.05 % Allowed : 16.22 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.21 % 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 (0.10), residues: 7290 helix: 1.59 (0.11), residues: 2100 sheet: -0.46 (0.09), residues: 3330 loop : -0.86 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 419 HIS 0.002 0.001 HIS C 635 PHE 0.020 0.001 PHE I 609 TYR 0.013 0.001 TYR J 600 ARG 0.003 0.000 ARG E 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13295.77 seconds wall clock time: 233 minutes 45.08 seconds (14025.08 seconds total)