Starting phenix.real_space_refine on Fri Dec 8 09:29:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/12_2023/5wq8_6676_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/12_2023/5wq8_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_6676/12_2023/5wq8_6676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/12_2023/5wq8_6676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/12_2023/5wq8_6676_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq8_6676/12_2023/5wq8_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 20.54, per 1000 atoms: 0.36 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: 15.41 Conformation dependent library (CDL) restraints added in 7.7 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: 24.29 Time building geometry restraints manager: 17.07 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: 12.370 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 112.850 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.320 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.510 ------------------------------------------------------------------------------- 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 : 4.858 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 1058 average time/residue: 0.5657 time to fit residues: 983.0622 Evaluate side-chains 590 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 580 time to evaluate : 4.638 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3793 time to fit residues: 13.8075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 375 optimal weight: 0.4980 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: 0.8980 chunk 667 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 340 GLN A 424 ASN A 428 ASN A 502 GLN A 640 GLN B 242 ASN B 288 HIS B 340 GLN B 424 ASN B 428 ASN B 502 GLN B 640 GLN C 242 ASN C 288 HIS C 340 GLN C 354 ASN C 428 ASN C 502 GLN D 242 ASN D 288 HIS D 340 GLN D 354 ASN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 428 ASN D 499 ASN D 502 GLN D 640 GLN E 242 ASN E 340 GLN E 424 ASN E 428 ASN E 640 GLN F 242 ASN 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 340 GLN G 424 ASN G 428 ASN G 502 GLN G 640 GLN H 242 ASN 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 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 424 ASN I 428 ASN I 502 GLN I 640 GLN J 242 ASN J 288 HIS J 336 ASN J 340 GLN J 424 ASN J 428 ASN J 533 GLN J 640 GLN K 242 ASN K 288 HIS K 340 GLN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 340 GLN ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 ASN M 428 ASN M 499 ASN M 502 GLN M 640 GLN N 242 ASN N 288 HIS N 300 GLN N 340 GLN N 428 ASN N 502 GLN N 640 GLN O 288 HIS O 340 GLN O 354 ASN O 424 ASN O 428 ASN O 502 GLN O 533 GLN O 640 GLN Total number of N/Q/H flips: 107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2639 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= 0.247 Angle : 0.710 8.501 76950 Z= 0.373 Chirality : 0.050 0.166 9405 Planarity : 0.005 0.075 10020 Dihedral : 6.090 22.956 7860 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.71 % Allowed : 8.96 % Favored : 88.32 % 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: -1.61 (0.09), residues: 7290 helix: -0.71 (0.11), residues: 2130 sheet: -1.06 (0.08), residues: 3210 loop : -0.93 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 419 HIS 0.003 0.002 HIS A 635 PHE 0.018 0.002 PHE G 609 TYR 0.017 0.002 TYR G 134 ARG 0.008 0.000 ARG A 598 *********************** 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 929 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 760 time to evaluate : 4.758 Fit side-chains outliers start: 169 outliers final: 59 residues processed: 895 average time/residue: 0.5058 time to fit residues: 791.6682 Evaluate side-chains 651 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 592 time to evaluate : 4.636 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.3902 time to fit residues: 51.0734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 555 optimal weight: 0.8980 chunk 454 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 668 optimal weight: 2.9990 chunk 722 optimal weight: 0.6980 chunk 595 optimal weight: 10.0000 chunk 663 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 536 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN C 511 ASN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN E 288 HIS E 511 ASN F 424 ASN G 300 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 511 ASN H 511 ASN I 242 ASN I 300 GLN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 511 ASN J 511 ASN K 242 ASN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 ASN L 502 GLN ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 511 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 56910 Z= 0.343 Angle : 0.679 10.014 76950 Z= 0.356 Chirality : 0.051 0.258 9405 Planarity : 0.005 0.065 10020 Dihedral : 5.729 21.295 7860 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.07 % Allowed : 10.23 % Favored : 86.70 % 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: -1.07 (0.09), residues: 7290 helix: 0.06 (0.11), residues: 2145 sheet: -0.88 (0.08), residues: 3240 loop : -0.81 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 419 HIS 0.003 0.001 HIS E 288 PHE 0.018 0.002 PHE F 609 TYR 0.012 0.002 TYR G 134 ARG 0.005 0.000 ARG D 209 *********************** 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 832 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 641 time to evaluate : 4.680 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 outliers start: 191 outliers final: 66 residues processed: 810 average time/residue: 0.5009 time to fit residues: 713.7776 Evaluate side-chains 650 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 584 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3962 time to fit residues: 56.9801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 2.9990 chunk 502 optimal weight: 0.2980 chunk 347 optimal weight: 5.9990 chunk 74 optimal weight: 0.0980 chunk 319 optimal weight: 4.9990 chunk 449 optimal weight: 9.9990 chunk 671 optimal weight: 0.6980 chunk 710 optimal weight: 9.9990 chunk 350 optimal weight: 7.9990 chunk 636 optimal weight: 0.2980 chunk 191 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 511 ASN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN G 340 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 GLN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 424 ASN J 424 ASN ** J 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 GLN ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 511 ASN N 354 ASN ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 242 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 56910 Z= 0.178 Angle : 0.587 8.409 76950 Z= 0.310 Chirality : 0.048 0.211 9405 Planarity : 0.004 0.056 10020 Dihedral : 5.091 19.079 7860 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.48 % Allowed : 11.55 % Favored : 86.97 % 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: -0.44 (0.10), residues: 7290 helix: 0.74 (0.11), residues: 2175 sheet: -0.55 (0.08), residues: 3225 loop : -0.68 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 419 HIS 0.002 0.001 HIS E 288 PHE 0.008 0.001 PHE M 450 TYR 0.010 0.001 TYR E 352 ARG 0.005 0.000 ARG O 616 *********************** 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 836 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 744 time to evaluate : 4.704 Fit side-chains outliers start: 92 outliers final: 34 residues processed: 815 average time/residue: 0.5211 time to fit residues: 746.9508 Evaluate side-chains 664 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 630 time to evaluate : 4.668 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4310 time to fit residues: 34.5622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 10 optimal weight: 30.0000 chunk 528 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 606 optimal weight: 1.9990 chunk 491 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 362 optimal weight: 2.9990 chunk 637 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 ASN C 502 GLN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 GLN H 524 ASN I 300 GLN I 340 GLN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 GLN J 336 ASN ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 ASN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 502 GLN ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 ASN O 502 GLN O 635 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 56910 Z= 0.456 Angle : 0.690 10.619 76950 Z= 0.360 Chirality : 0.051 0.329 9405 Planarity : 0.005 0.070 10020 Dihedral : 5.460 22.970 7860 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.96 % Allowed : 13.77 % Favored : 84.27 % 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: -0.53 (0.10), residues: 7290 helix: 0.84 (0.11), residues: 2100 sheet: -0.64 (0.08), residues: 3315 loop : -0.81 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 419 HIS 0.003 0.001 HIS I 635 PHE 0.023 0.002 PHE E 609 TYR 0.011 0.002 TYR J 600 ARG 0.005 0.000 ARG E 477 *********************** 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 712 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 590 time to evaluate : 4.684 Fit side-chains outliers start: 122 outliers final: 58 residues processed: 690 average time/residue: 0.5030 time to fit residues: 609.2821 Evaluate side-chains 598 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 540 time to evaluate : 4.656 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4230 time to fit residues: 52.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 0.9980 chunk 639 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 417 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 711 optimal weight: 5.9990 chunk 590 optimal weight: 3.9990 chunk 329 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 373 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 GLN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 GLN ** I 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 56910 Z= 0.257 Angle : 0.604 9.824 76950 Z= 0.316 Chirality : 0.048 0.208 9405 Planarity : 0.004 0.056 10020 Dihedral : 5.112 20.864 7860 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.06 % Favored : 96.74 % Rotamer: Outliers : 1.12 % Allowed : 15.87 % Favored : 83.00 % 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: -0.27 (0.10), residues: 7290 helix: 1.15 (0.11), residues: 2100 sheet: -0.50 (0.08), residues: 3315 loop : -0.76 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 419 HIS 0.002 0.000 HIS C 635 PHE 0.012 0.001 PHE O 580 TYR 0.010 0.001 TYR A 352 ARG 0.013 0.000 ARG H 616 *********************** 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 695 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 625 time to evaluate : 4.658 Fit side-chains outliers start: 70 outliers final: 35 residues processed: 678 average time/residue: 0.4927 time to fit residues: 593.4006 Evaluate side-chains 615 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 580 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4010 time to fit residues: 33.4056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 405 optimal weight: 2.9990 chunk 519 optimal weight: 3.9990 chunk 402 optimal weight: 0.6980 chunk 598 optimal weight: 3.9990 chunk 397 optimal weight: 20.0000 chunk 708 optimal weight: 0.9990 chunk 443 optimal weight: 7.9990 chunk 431 optimal weight: 2.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 ASN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4106 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= 0.252 Angle : 0.601 10.702 76950 Z= 0.313 Chirality : 0.048 0.180 9405 Planarity : 0.004 0.054 10020 Dihedral : 4.996 20.761 7860 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.39 % Favored : 96.41 % Rotamer: Outliers : 1.32 % Allowed : 16.48 % Favored : 82.20 % 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: -0.15 (0.10), residues: 7290 helix: 1.32 (0.11), residues: 2100 sheet: -0.43 (0.09), residues: 3315 loop : -0.81 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 419 HIS 0.002 0.000 HIS A 635 PHE 0.018 0.001 PHE F 609 TYR 0.010 0.001 TYR J 600 ARG 0.003 0.000 ARG D 222 *********************** 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 697 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 615 time to evaluate : 4.796 Fit side-chains outliers start: 82 outliers final: 38 residues processed: 678 average time/residue: 0.4980 time to fit residues: 596.8582 Evaluate side-chains 611 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 573 time to evaluate : 4.683 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4152 time to fit residues: 36.1186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 423 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 450 optimal weight: 6.9990 chunk 482 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 556 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 GLN ** H 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4219 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= 0.262 Angle : 0.599 8.368 76950 Z= 0.313 Chirality : 0.048 0.179 9405 Planarity : 0.004 0.054 10020 Dihedral : 4.965 21.009 7860 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.43 % Favored : 96.36 % Rotamer: Outliers : 0.95 % Allowed : 17.25 % Favored : 81.80 % 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: -0.10 (0.10), residues: 7290 helix: 1.49 (0.11), residues: 2070 sheet: -0.40 (0.09), residues: 3315 loop : -0.92 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 419 HIS 0.002 0.000 HIS C 635 PHE 0.012 0.001 PHE D 204 TYR 0.010 0.001 TYR N 600 ARG 0.013 0.000 ARG M 616 *********************** 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 672 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 613 time to evaluate : 4.683 Fit side-chains outliers start: 59 outliers final: 29 residues processed: 660 average time/residue: 0.5040 time to fit residues: 588.5477 Evaluate side-chains 608 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 579 time to evaluate : 4.765 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4363 time to fit residues: 30.3068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 0.9990 chunk 678 optimal weight: 2.9990 chunk 619 optimal weight: 0.9980 chunk 660 optimal weight: 1.9990 chunk 397 optimal weight: 20.0000 chunk 287 optimal weight: 2.9990 chunk 518 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 596 optimal weight: 9.9990 chunk 624 optimal weight: 0.7980 chunk 657 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 304 ASN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 524 ASN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 56910 Z= 0.344 Angle : 0.639 12.037 76950 Z= 0.332 Chirality : 0.049 0.279 9405 Planarity : 0.005 0.057 10020 Dihedral : 5.118 22.526 7860 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.79 % Favored : 96.01 % Rotamer: Outliers : 0.79 % Allowed : 17.67 % Favored : 81.54 % 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: -0.21 (0.10), residues: 7290 helix: 1.31 (0.11), residues: 2100 sheet: -0.43 (0.09), residues: 3315 loop : -0.95 (0.13), residues: 1875 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 0.022 0.001 PHE I 609 TYR 0.012 0.001 TYR J 600 ARG 0.013 0.000 ARG M 616 *********************** 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 626 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 577 time to evaluate : 4.852 Fit side-chains outliers start: 49 outliers final: 26 residues processed: 607 average time/residue: 0.5055 time to fit residues: 540.8536 Evaluate side-chains 577 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 551 time to evaluate : 4.944 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4276 time to fit residues: 27.7398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 2.9990 chunk 698 optimal weight: 5.9990 chunk 426 optimal weight: 0.9990 chunk 331 optimal weight: 1.9990 chunk 485 optimal weight: 0.8980 chunk 732 optimal weight: 1.9990 chunk 673 optimal weight: 0.3980 chunk 583 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 450 optimal weight: 0.9980 chunk 357 optimal weight: 0.3980 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 304 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 GLN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 502 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4415 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= 0.221 Angle : 0.595 12.731 76950 Z= 0.309 Chirality : 0.048 0.210 9405 Planarity : 0.004 0.053 10020 Dihedral : 4.887 20.259 7860 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.68 % Rotamer: Outliers : 0.31 % Allowed : 17.99 % Favored : 81.70 % 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: -0.00 (0.10), residues: 7290 helix: 1.56 (0.11), residues: 2070 sheet: -0.28 (0.09), residues: 3225 loop : -0.98 (0.13), residues: 1995 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 0.010 0.001 TYR C 600 ARG 0.012 0.000 ARG M 616 ********************** 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 632 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 613 time to evaluate : 4.834 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 625 average time/residue: 0.4947 time to fit residues: 549.9062 Evaluate side-chains 584 residues out of total 6225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 578 time to evaluate : 4.648 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4035 time to fit residues: 11.2410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 2.9990 chunk 621 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 537 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 0.0070 chunk 584 optimal weight: 0.1980 chunk 244 optimal weight: 0.1980 chunk 599 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 502 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN H 524 ASN ** J 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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** ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 524 ASN O 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.200176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123636 restraints weight = 57584.227| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.12 r_work: 0.3161 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 56910 Z= 0.173 Angle : 0.571 9.080 76950 Z= 0.298 Chirality : 0.047 0.208 9405 Planarity : 0.004 0.053 10020 Dihedral : 4.685 19.803 7860 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.58 % Rotamer: Outliers : 0.22 % Allowed : 18.25 % Favored : 81.53 % 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: 0.01 (0.10), residues: 7290 helix: 1.37 (0.11), residues: 2220 sheet: -0.26 (0.09), residues: 3270 loop : -0.93 (0.14), residues: 1800 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 0.017 0.001 PHE I 609 TYR 0.010 0.001 TYR C 600 ARG 0.012 0.000 ARG M 616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12572.86 seconds wall clock time: 221 minutes 39.75 seconds (13299.75 seconds total)