Starting phenix.real_space_refine (version: dev) on Mon Feb 27 22:43:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzn_23083/02_2023/7kzn_23083.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzn_23083/02_2023/7kzn_23083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzn_23083/02_2023/7kzn_23083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzn_23083/02_2023/7kzn_23083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzn_23083/02_2023/7kzn_23083.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kzn_23083/02_2023/7kzn_23083.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "B ARG 385": "NH1" <-> "NH2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 514": "OE1" <-> "OE2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "C GLU 763": "OE1" <-> "OE2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C GLU 822": "OE1" <-> "OE2" Residue "C GLU 841": "OE1" <-> "OE2" Residue "C GLU 917": "OE1" <-> "OE2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 956": "NH1" <-> "NH2" Residue "C GLU 977": "OE1" <-> "OE2" Residue "C GLU 1050": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D GLU 659": "OE1" <-> "OE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 263": "NH1" <-> "NH2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E GLU 299": "OE1" <-> "OE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 353": "NH1" <-> "NH2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E GLU 442": "OE1" <-> "OE2" Residue "E ARG 505": "NH1" <-> "NH2" Residue "E GLU 537": "OE1" <-> "OE2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I ARG 73": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I ARG 89": "NH1" <-> "NH2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "J ARG 59": "NH1" <-> "NH2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 32": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 85": "NH1" <-> "NH2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "Z GLU 8": "OE1" <-> "OE2" Residue "Z ARG 12": "NH1" <-> "NH2" Residue "Z GLU 41": "OE1" <-> "OE2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "Z ARG 123": "NH1" <-> "NH2" Residue "Z GLU 134": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31205 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1544 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PTRANS': 19, 'TRANS': 295} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1037 Unresolved non-hydrogen angles: 1346 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 9, 'TYR:plan': 12, 'ASN:plan1': 15, 'TRP:plan': 10, 'ASP:plan': 23, 'PHE:plan': 18, 'GLU:plan': 18, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 626 Chain: "B" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5028 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 15, 'TRANS': 667} Chain breaks: 17 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 293 Chain: "C" Number of atoms: 7293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7293 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 26, 'TRANS': 938} Chain breaks: 19 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 584 Unresolved non-hydrogen angles: 745 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 302 Chain: "D" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3609 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 2 Chain: "E" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3697 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 24, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 495 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 1, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 203 Chain: "G" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain breaks: 1 Chain: "H" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 451 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 8, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 175 Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "J" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "K" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 671 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "L" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 671 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "M" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 671 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "N" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 407 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 167 Chain: "O" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 481 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 154 Chain: "P" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "X" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "Y" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 840 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 168 Planarities with less than four sites: {'UNK:plan-1': 168} Unresolved non-hydrogen planarities: 168 Chain: "Z" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Time building chain proxies: 17.56, per 1000 atoms: 0.56 Number of scatterers: 31205 At special positions: 0 Unit cell: (202.64, 224.4, 277.44, 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 143 16.00 O 5987 8.00 N 5530 7.00 C 19545 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: 12.86 Conformation dependent library (CDL) restraints added in 4.9 seconds 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8386 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 54.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.385A pdb=" N TRP A 62 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.667A pdb=" N VAL A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 293 " --> pdb=" O ALA A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 293' Processing helix chain 'B' and resid 17 through 33 removed outlier: 3.738A pdb=" N LYS B 33 " --> pdb=" O CYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 45 through 56 removed outlier: 4.604A pdb=" N THR B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 125 removed outlier: 3.524A pdb=" N THR B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.532A pdb=" N LEU B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 142 through 162 removed outlier: 4.020A pdb=" N LYS B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 218 removed outlier: 4.826A pdb=" N TRP B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 272 through 299 removed outlier: 4.156A pdb=" N ALA B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.979A pdb=" N MET B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.541A pdb=" N VAL B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 405 removed outlier: 4.213A pdb=" N LYS B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 441 Processing helix chain 'B' and resid 454 through 475 Processing helix chain 'B' and resid 489 through 504 removed outlier: 3.930A pdb=" N ASP B 493 " --> pdb=" O GLN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'B' and resid 541 through 570 removed outlier: 6.308A pdb=" N LYS B 547 " --> pdb=" O HIS B 543 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 548 " --> pdb=" O ASP B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 605 Proline residue: B 600 - end of helix Processing helix chain 'B' and resid 615 through 654 removed outlier: 4.391A pdb=" N GLU B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 626 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 695 Processing helix chain 'B' and resid 730 through 742 Processing helix chain 'B' and resid 742 through 759 removed outlier: 3.685A pdb=" N ILE B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 772 Processing helix chain 'B' and resid 774 through 784 Processing helix chain 'B' and resid 795 through 826 removed outlier: 3.675A pdb=" N LEU B 826 " --> pdb=" O THR B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 866 removed outlier: 4.023A pdb=" N ALA B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 906 Processing helix chain 'C' and resid 2 through 19 removed outlier: 3.715A pdb=" N ARG C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 31 removed outlier: 3.587A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.668A pdb=" N PHE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 removed outlier: 3.561A pdb=" N LYS C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 4.470A pdb=" N MET C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 164 removed outlier: 4.003A pdb=" N ALA C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.627A pdb=" N THR C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TRP C 210 " --> pdb=" O CYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 254 removed outlier: 3.849A pdb=" N LEU C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 272 through 300 removed outlier: 3.642A pdb=" N LEU C 300 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 309 removed outlier: 3.771A pdb=" N GLN C 309 " --> pdb=" O PRO C 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.805A pdb=" N GLU C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 339 through 362 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 414 through 440 removed outlier: 4.028A pdb=" N LEU C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 Processing helix chain 'C' and resid 454 through 467 removed outlier: 3.871A pdb=" N VAL C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 506 removed outlier: 4.025A pdb=" N ASP C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C 486 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 527 removed outlier: 3.678A pdb=" N ALA C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 539 through 561 removed outlier: 4.120A pdb=" N ASN C 546 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 590 removed outlier: 3.766A pdb=" N ALA C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 639 removed outlier: 4.146A pdb=" N LYS C 618 " --> pdb=" O ASN C 614 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 639 " --> pdb=" O ILE C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 677 removed outlier: 5.202A pdb=" N MET C 674 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN C 675 " --> pdb=" O LYS C 672 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 676 " --> pdb=" O TYR C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 703 removed outlier: 3.663A pdb=" N THR C 703 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.932A pdb=" N GLU C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS C 711 " --> pdb=" O ARG C 707 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 712 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 725 through 735 removed outlier: 3.862A pdb=" N ASP C 729 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET C 730 " --> pdb=" O HIS C 726 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 733 " --> pdb=" O ASP C 729 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 735 " --> pdb=" O GLU C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 772 removed outlier: 3.689A pdb=" N ARG C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 762 " --> pdb=" O GLY C 758 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 767 " --> pdb=" O GLU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 removed outlier: 3.798A pdb=" N THR C 787 " --> pdb=" O ILE C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 837 removed outlier: 3.564A pdb=" N LYS C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 813 " --> pdb=" O PHE C 809 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 814 " --> pdb=" O GLN C 810 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 815 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU C 829 " --> pdb=" O ARG C 825 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 844 removed outlier: 3.831A pdb=" N GLU C 844 " --> pdb=" O GLU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 882 Processing helix chain 'C' and resid 915 through 935 removed outlier: 3.571A pdb=" N GLN C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 979 Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 994 through 1002 Processing helix chain 'C' and resid 1008 through 1031 Processing helix chain 'C' and resid 1042 through 1076 removed outlier: 3.790A pdb=" N LEU C1047 " --> pdb=" O LEU C1043 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C1056 " --> pdb=" O VAL C1052 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C1065 " --> pdb=" O ASN C1061 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C1076 " --> pdb=" O LEU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1101 removed outlier: 3.922A pdb=" N LYS C1101 " --> pdb=" O MET C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1121 Proline residue: C1116 - end of helix Processing helix chain 'C' and resid 1138 through 1159 removed outlier: 3.877A pdb=" N LEU C1149 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS C1150 " --> pdb=" O TRP C1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 221 Processing helix chain 'D' and resid 249 through 252 Processing helix chain 'D' and resid 253 through 270 removed outlier: 3.838A pdb=" N ASN D 270 " --> pdb=" O MET D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.596A pdb=" N TRP D 282 " --> pdb=" O ASP D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 675 removed outlier: 3.518A pdb=" N LEU D 658 " --> pdb=" O LYS D 654 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 675 " --> pdb=" O ARG D 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 102 removed outlier: 3.864A pdb=" N ARG E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 127 removed outlier: 4.381A pdb=" N VAL E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 490 through 495 Processing helix chain 'E' and resid 497 through 499 No H-bonds generated for 'chain 'E' and resid 497 through 499' Processing helix chain 'E' and resid 500 through 517 removed outlier: 3.626A pdb=" N LEU E 509 " --> pdb=" O ARG E 505 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU E 510 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS E 511 " --> pdb=" O LYS E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 549 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 59 through 76 Processing helix chain 'G' and resid 17 through 31 removed outlier: 3.712A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 50 Processing helix chain 'G' and resid 57 through 67 Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.739A pdb=" N SER G 90 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 removed outlier: 3.697A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 110 Processing helix chain 'G' and resid 117 through 128 removed outlier: 3.942A pdb=" N LEU G 121 " --> pdb=" O LEU G 117 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 128 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 141 removed outlier: 3.620A pdb=" N LYS G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 158 Processing helix chain 'H' and resid 29 through 47 Processing helix chain 'H' and resid 49 through 61 Processing helix chain 'I' and resid 3 through 16 Processing helix chain 'I' and resid 38 through 64 removed outlier: 3.623A pdb=" N THR I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 12 Processing helix chain 'J' and resid 39 through 60 Proline residue: J 48 - end of helix Processing helix chain 'K' and resid 16 through 34 removed outlier: 4.017A pdb=" N ASP K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA K 30 " --> pdb=" O CYS K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 50 removed outlier: 3.922A pdb=" N ALA K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE K 48 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 34 removed outlier: 4.558A pdb=" N GLN L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA L 30 " --> pdb=" O CYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 52 removed outlier: 4.561A pdb=" N LYS L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 34 removed outlier: 4.048A pdb=" N ALA M 30 " --> pdb=" O CYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 52 removed outlier: 3.652A pdb=" N ILE M 40 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.874A pdb=" N ASP N 25 " --> pdb=" O ALA N 21 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA N 30 " --> pdb=" O CYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 52 removed outlier: 3.702A pdb=" N GLU N 47 " --> pdb=" O TYR N 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 33 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 42 through 62 removed outlier: 3.662A pdb=" N MET O 61 " --> pdb=" O ARG O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 16 removed outlier: 3.911A pdb=" N PHE P 12 " --> pdb=" O ASP P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 45 Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'X' and resid 321 through 345 removed outlier: 4.161A pdb=" N UNK X 329 " --> pdb=" O UNK X 325 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N UNK X 330 " --> pdb=" O UNK X 326 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N UNK X 345 " --> pdb=" O UNK X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 395 removed outlier: 3.528A pdb=" N UNK X 353 " --> pdb=" O UNK X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 404 through 448 Processing helix chain 'Y' and resid 271 through 278 Processing helix chain 'Y' and resid 285 through 294 removed outlier: 4.387A pdb=" N UNK Y 292 " --> pdb=" O UNK Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 295 through 383 removed outlier: 4.252A pdb=" N UNK Y 299 " --> pdb=" O UNK Y 295 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N UNK Y 301 " --> pdb=" O UNK Y 297 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N UNK Y 310 " --> pdb=" O UNK Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 395 through 410 Processing helix chain 'Y' and resid 425 through 444 Processing helix chain 'Z' and resid 7 through 27 removed outlier: 3.748A pdb=" N ALA Z 11 " --> pdb=" O ARG Z 7 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN Z 14 " --> pdb=" O TYR Z 10 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN Z 17 " --> pdb=" O LYS Z 13 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU Z 18 " --> pdb=" O ASN Z 14 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG Z 21 " --> pdb=" O ASN Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 35 through 47 Processing helix chain 'Z' and resid 72 through 81 removed outlier: 3.582A pdb=" N THR Z 80 " --> pdb=" O GLN Z 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG Z 81 " --> pdb=" O THR Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 104 removed outlier: 4.048A pdb=" N VAL Z 98 " --> pdb=" O LEU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 113 through 120 removed outlier: 3.880A pdb=" N MET Z 117 " --> pdb=" O LEU Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 126 through 133 removed outlier: 3.712A pdb=" N GLN Z 132 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 5.927A pdb=" N GLY A 34 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ASP A 48 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 4.225A pdb=" N LYS A 199 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 218 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU A 201 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N HIS A 216 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N MET A 203 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP A 214 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 205 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 302 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.703A pdb=" N ILE B 107 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AB1, first strand: chain 'D' and resid 181 through 185 removed outlier: 3.556A pdb=" N VAL L 68 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE M 85 " --> pdb=" O PHE M 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 193 through 200 removed outlier: 7.730A pdb=" N ASN K 63 " --> pdb=" O LYS P 74 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE P 76 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY K 61 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR P 78 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE K 59 " --> pdb=" O TYR P 78 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE P 80 " --> pdb=" O HIS K 57 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS K 57 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE K 85 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE K 75 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA K 13 " --> pdb=" O PHE K 75 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR K 77 " --> pdb=" O LYS K 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 72 through 76 removed outlier: 7.732A pdb=" N HIS K 57 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE P 80 " --> pdb=" O HIS K 57 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE K 59 " --> pdb=" O TYR P 78 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR P 78 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY K 61 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE P 76 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN K 63 " --> pdb=" O LYS P 74 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU P 87 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR P 24 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR P 89 " --> pdb=" O LYS P 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 297 through 302 removed outlier: 5.483A pdb=" N SER D 636 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG D 301 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL D 634 " --> pdb=" O ARG D 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 342 through 344 removed outlier: 4.013A pdb=" N ILE D 342 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 344 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 355 " --> pdb=" O ILE D 344 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 366 through 368 Processing sheet with id=AB7, first strand: chain 'D' and resid 416 through 418 removed outlier: 4.012A pdb=" N GLN D 427 " --> pdb=" O GLN D 418 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 448 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 482 through 484 Processing sheet with id=AB9, first strand: chain 'D' and resid 523 through 527 removed outlier: 6.680A pdb=" N ALA D 539 " --> pdb=" O TYR D 524 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL D 526 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 537 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 540 " --> pdb=" O ASP D 544 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS D 545 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 567 through 572 removed outlier: 6.648A pdb=" N VAL D 583 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL D 570 " --> pdb=" O ALA D 581 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 584 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG D 588 " --> pdb=" O THR D 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 62 through 64 removed outlier: 4.684A pdb=" N TYR M 67 " --> pdb=" O CYS L 58 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N CYS L 58 " --> pdb=" O TYR M 67 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE L 85 " --> pdb=" O PHE L 78 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE L 75 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA L 13 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR L 77 " --> pdb=" O LYS L 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 152 through 154 removed outlier: 4.259A pdb=" N THR E 152 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 477 " --> pdb=" O THR E 152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 163 through 169 removed outlier: 6.765A pdb=" N ALA E 181 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL E 167 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR E 199 " --> pdb=" O VAL E 180 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 232 through 234 removed outlier: 3.931A pdb=" N ALA E 234 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA E 242 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 330 through 333 removed outlier: 3.928A pdb=" N ILE E 340 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 369 through 370 removed outlier: 3.851A pdb=" N ARG E 369 " --> pdb=" O LEU E 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 421 through 423 Processing sheet with id=AC9, first strand: chain 'F' and resid 83 through 93 Processing sheet with id=AD1, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AD2, first strand: chain 'I' and resid 22 through 25 removed outlier: 3.938A pdb=" N GLY J 19 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 57 through 61 Processing sheet with id=AD4, first strand: chain 'O' and resid 65 through 75 Processing sheet with id=AD5, first strand: chain 'Z' and resid 33 through 34 removed outlier: 4.017A pdb=" N ILE Z 70 " --> pdb=" O ILE Z 34 " (cutoff:3.500A) 1884 hydrogen bonds defined for protein. 5430 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: 12.05 Time building geometry restraints manager: 13.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5648 1.32 - 1.44: 7793 1.44 - 1.57: 17958 1.57 - 1.70: 6 1.70 - 1.83: 233 Bond restraints: 31638 Sorted by residual: bond pdb=" CA SER D 314 " pdb=" CB SER D 314 " ideal model delta sigma weight residual 1.533 1.439 0.094 1.72e-02 3.38e+03 2.96e+01 bond pdb=" N LEU D 299 " pdb=" CA LEU D 299 " ideal model delta sigma weight residual 1.458 1.483 -0.025 6.30e-03 2.52e+04 1.55e+01 bond pdb=" C THR E 278 " pdb=" O THR E 278 " ideal model delta sigma weight residual 1.234 1.189 0.044 1.24e-02 6.50e+03 1.27e+01 bond pdb=" N VAL D 429 " pdb=" CA VAL D 429 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" N GLN D 427 " pdb=" CA GLN D 427 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.23e-02 6.61e+03 1.21e+01 ... (remaining 31633 not shown) Histogram of bond angle deviations from ideal: 91.72 - 100.47: 49 100.47 - 109.22: 3165 109.22 - 117.97: 20682 117.97 - 126.73: 18742 126.73 - 135.48: 318 Bond angle restraints: 42956 Sorted by residual: angle pdb=" CA PRO C 129 " pdb=" N PRO C 129 " pdb=" CD PRO C 129 " ideal model delta sigma weight residual 112.00 100.72 11.28 1.40e+00 5.10e-01 6.50e+01 angle pdb=" CB MET C 455 " pdb=" CG MET C 455 " pdb=" SD MET C 455 " ideal model delta sigma weight residual 112.70 91.72 20.98 3.00e+00 1.11e-01 4.89e+01 angle pdb=" CA ARG C 586 " pdb=" CB ARG C 586 " pdb=" CG ARG C 586 " ideal model delta sigma weight residual 114.10 127.85 -13.75 2.00e+00 2.50e-01 4.73e+01 angle pdb=" CB ARG B 603 " pdb=" CG ARG B 603 " pdb=" CD ARG B 603 " ideal model delta sigma weight residual 111.30 127.04 -15.74 2.30e+00 1.89e-01 4.68e+01 angle pdb=" N ARG D 184 " pdb=" CA ARG D 184 " pdb=" CB ARG D 184 " ideal model delta sigma weight residual 111.62 122.09 -10.47 1.62e+00 3.81e-01 4.18e+01 ... (remaining 42951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.51: 17183 18.51 - 37.03: 1587 37.03 - 55.54: 196 55.54 - 74.05: 43 74.05 - 92.57: 24 Dihedral angle restraints: 19033 sinusoidal: 6210 harmonic: 12823 Sorted by residual: dihedral pdb=" C THR D 313 " pdb=" N THR D 313 " pdb=" CA THR D 313 " pdb=" CB THR D 313 " ideal model delta harmonic sigma weight residual -122.00 -140.06 18.06 0 2.50e+00 1.60e-01 5.22e+01 dihedral pdb=" CA GLY E 473 " pdb=" C GLY E 473 " pdb=" N CYS E 474 " pdb=" CA CYS E 474 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA CYS E 343 " pdb=" C CYS E 343 " pdb=" N ASN E 344 " pdb=" CA ASN E 344 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 19030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4678 0.130 - 0.261: 340 0.261 - 0.391: 27 0.391 - 0.522: 3 0.522 - 0.652: 3 Chirality restraints: 5051 Sorted by residual: chirality pdb=" CA THR D 313 " pdb=" N THR D 313 " pdb=" C THR D 313 " pdb=" CB THR D 313 " both_signs ideal model delta sigma weight residual False 2.53 1.87 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE D 342 " pdb=" CA ILE D 342 " pdb=" CG1 ILE D 342 " pdb=" CG2 ILE D 342 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB VAL D 558 " pdb=" CA VAL D 558 " pdb=" CG1 VAL D 558 " pdb=" CG2 VAL D 558 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 5048 not shown) Planarity restraints: 5639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 290 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO D 291 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO D 291 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 291 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 755 " 0.041 2.00e-02 2.50e+03 3.88e-02 2.64e+01 pdb=" CG PHE C 755 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 PHE C 755 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 755 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 755 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 755 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE C 755 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 230 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ASN E 230 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN E 230 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU E 231 " 0.026 2.00e-02 2.50e+03 ... (remaining 5636 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3795 2.74 - 3.28: 31638 3.28 - 3.82: 50095 3.82 - 4.36: 55191 4.36 - 4.90: 92503 Nonbonded interactions: 233222 Sorted by model distance: nonbonded pdb=" O SER D 304 " pdb=" OG SER D 307 " model vdw 2.202 2.440 nonbonded pdb=" ND2 ASN E 168 " pdb=" O ALA E 222 " model vdw 2.209 2.520 nonbonded pdb=" OG SER G 71 " pdb=" O CYS G 73 " model vdw 2.212 2.440 nonbonded pdb=" O ASP C 830 " pdb=" OG1 THR C 833 " model vdw 2.219 2.440 nonbonded pdb=" O GLN E 112 " pdb=" OG SER E 115 " model vdw 2.222 2.440 ... (remaining 233217 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 'K' and ((resid 8 through 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 or (resid 66 through 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 or (resid 82 through 89 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 8 through 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 or (resid 66 through 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 or (resid 82 through 89 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and ((resid 8 through 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 or (resid 66 through 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 or (resid 82 through 89 and ( \ name N or name CA or name C or name O or name CB )))) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 19545 2.51 5 N 5530 2.21 5 O 5987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.790 Check model and map are aligned: 0.460 Process input model: 80.990 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.300 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 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 : 0.010 0.135 31638 Z= 0.663 Angle : 1.357 20.981 42956 Z= 0.742 Chirality : 0.074 0.652 5051 Planarity : 0.010 0.131 5639 Dihedral : 14.785 92.568 10647 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.96 % Favored : 89.81 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.12), residues: 3985 helix: -1.15 (0.11), residues: 1866 sheet: -2.30 (0.22), residues: 500 loop : -3.23 (0.13), residues: 1619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 530 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 540 average time/residue: 0.4470 time to fit residues: 383.4787 Evaluate side-chains 430 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 426 time to evaluate : 3.711 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2933 time to fit residues: 7.1422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 363 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 337 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 251 optimal weight: 0.5980 chunk 391 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS C 403 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN C 546 ASN D 270 ASN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 207 ASN E 273 GLN ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 31638 Z= 0.224 Angle : 0.734 17.037 42956 Z= 0.388 Chirality : 0.045 0.227 5051 Planarity : 0.005 0.082 5639 Dihedral : 6.237 25.932 4585 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 3985 helix: -0.11 (0.12), residues: 1887 sheet: -1.94 (0.23), residues: 489 loop : -3.24 (0.13), residues: 1609 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 487 time to evaluate : 3.664 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 outliers start: 52 outliers final: 26 residues processed: 511 average time/residue: 0.4508 time to fit residues: 365.9539 Evaluate side-chains 470 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 444 time to evaluate : 3.803 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2821 time to fit residues: 18.7932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 217 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 266 optimal weight: 0.0070 chunk 107 optimal weight: 40.0000 chunk 392 optimal weight: 20.0000 chunk 423 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 388 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 314 optimal weight: 0.1980 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN D 270 ASN D 520 HIS ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 31638 Z= 0.231 Angle : 0.690 17.186 42956 Z= 0.361 Chirality : 0.044 0.212 5051 Planarity : 0.005 0.071 5639 Dihedral : 5.756 25.420 4585 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.90 % Favored : 92.05 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3985 helix: 0.33 (0.12), residues: 1898 sheet: -1.86 (0.23), residues: 493 loop : -3.16 (0.13), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 483 time to evaluate : 3.863 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: 61 outliers final: 28 residues processed: 524 average time/residue: 0.4531 time to fit residues: 376.5451 Evaluate side-chains 481 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 453 time to evaluate : 3.689 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3031 time to fit residues: 20.6762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 387 optimal weight: 0.0010 chunk 294 optimal weight: 50.0000 chunk 203 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 0.5980 chunk 393 optimal weight: 10.0000 chunk 416 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 372 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 overall best weight: 3.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN K 20 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 31638 Z= 0.362 Angle : 0.775 19.965 42956 Z= 0.406 Chirality : 0.047 0.231 5051 Planarity : 0.005 0.066 5639 Dihedral : 5.969 28.029 4585 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.16 % Favored : 90.79 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3985 helix: 0.33 (0.12), residues: 1905 sheet: -1.89 (0.22), residues: 524 loop : -3.23 (0.13), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 472 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 58 residues processed: 535 average time/residue: 0.4430 time to fit residues: 379.9689 Evaluate side-chains 505 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 447 time to evaluate : 3.642 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.3037 time to fit residues: 37.8746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 346 optimal weight: 9.9990 chunk 236 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 171 optimal weight: 0.6980 chunk 355 optimal weight: 6.9990 chunk 287 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 212 optimal weight: 0.9980 chunk 373 optimal weight: 30.0000 chunk 105 optimal weight: 30.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS D 270 ASN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 20 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 31638 Z= 0.295 Angle : 0.723 19.170 42956 Z= 0.378 Chirality : 0.045 0.247 5051 Planarity : 0.005 0.066 5639 Dihedral : 5.754 25.958 4585 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.58 % Favored : 91.37 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 3985 helix: 0.49 (0.12), residues: 1912 sheet: -1.95 (0.23), residues: 516 loop : -3.18 (0.13), residues: 1557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 475 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 32 residues processed: 515 average time/residue: 0.4627 time to fit residues: 376.7765 Evaluate side-chains 474 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 442 time to evaluate : 3.859 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2714 time to fit residues: 21.6275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 140 optimal weight: 10.0000 chunk 375 optimal weight: 50.0000 chunk 82 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 417 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 570 ASN D 270 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.107 31638 Z= 0.406 Angle : 0.805 21.922 42956 Z= 0.422 Chirality : 0.048 0.270 5051 Planarity : 0.006 0.067 5639 Dihedral : 6.006 26.884 4585 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.14 % Favored : 89.81 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 3985 helix: 0.37 (0.12), residues: 1909 sheet: -2.03 (0.22), residues: 518 loop : -3.26 (0.13), residues: 1558 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 460 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 53 residues processed: 518 average time/residue: 0.4553 time to fit residues: 377.0149 Evaluate side-chains 490 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 437 time to evaluate : 3.847 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2909 time to fit residues: 33.6784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 402 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 351 optimal weight: 8.9990 chunk 232 optimal weight: 0.9980 chunk 415 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 253 optimal weight: 0.4980 chunk 191 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 570 ASN D 270 ASN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS G 65 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 31638 Z= 0.235 Angle : 0.701 18.329 42956 Z= 0.362 Chirality : 0.044 0.291 5051 Planarity : 0.005 0.070 5639 Dihedral : 5.542 25.350 4585 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.70 % Favored : 92.27 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3985 helix: 0.69 (0.12), residues: 1912 sheet: -1.85 (0.23), residues: 502 loop : -3.18 (0.13), residues: 1571 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 469 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 23 residues processed: 503 average time/residue: 0.4722 time to fit residues: 381.4746 Evaluate side-chains 472 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 449 time to evaluate : 3.504 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3107 time to fit residues: 18.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 256 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 38 optimal weight: 50.0000 chunk 326 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 570 ASN D 270 ASN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 31638 Z= 0.290 Angle : 0.739 18.944 42956 Z= 0.381 Chirality : 0.045 0.268 5051 Planarity : 0.005 0.072 5639 Dihedral : 5.596 24.825 4585 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.34 % Favored : 90.64 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3985 helix: 0.69 (0.12), residues: 1914 sheet: -1.86 (0.23), residues: 517 loop : -3.20 (0.13), residues: 1554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 460 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 490 average time/residue: 0.4571 time to fit residues: 357.6307 Evaluate side-chains 472 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 443 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3275 time to fit residues: 21.6898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 377 optimal weight: 50.0000 chunk 397 optimal weight: 9.9990 chunk 363 optimal weight: 30.0000 chunk 387 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 303 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 349 optimal weight: 0.7980 chunk 366 optimal weight: 7.9990 chunk 385 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS D 270 ASN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 31638 Z= 0.217 Angle : 0.700 16.453 42956 Z= 0.358 Chirality : 0.043 0.245 5051 Planarity : 0.004 0.073 5639 Dihedral : 5.311 23.826 4585 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.13 % Favored : 92.85 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 3985 helix: 0.87 (0.12), residues: 1915 sheet: -1.74 (0.23), residues: 516 loop : -3.10 (0.14), residues: 1554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 468 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 489 average time/residue: 0.4526 time to fit residues: 354.3694 Evaluate side-chains 457 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 442 time to evaluate : 3.848 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3213 time to fit residues: 14.1580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 254 optimal weight: 0.9990 chunk 409 optimal weight: 9.9990 chunk 249 optimal weight: 0.7980 chunk 194 optimal weight: 40.0000 chunk 284 optimal weight: 0.3980 chunk 429 optimal weight: 10.0000 chunk 395 optimal weight: 30.0000 chunk 341 optimal weight: 8.9990 chunk 35 optimal weight: 40.0000 chunk 264 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS D 270 ASN D 409 ASN D 545 HIS ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** Z 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 31638 Z= 0.189 Angle : 0.682 15.197 42956 Z= 0.346 Chirality : 0.043 0.278 5051 Planarity : 0.004 0.073 5639 Dihedral : 5.049 22.064 4585 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3985 helix: 1.04 (0.12), residues: 1921 sheet: -1.64 (0.23), residues: 516 loop : -2.99 (0.14), residues: 1548 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 464 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 473 average time/residue: 0.4547 time to fit residues: 342.5189 Evaluate side-chains 451 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 446 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2843 time to fit residues: 7.8365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 271 optimal weight: 3.9990 chunk 364 optimal weight: 40.0000 chunk 104 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 50.0000 chunk 342 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 43 optimal weight: 0.0050 chunk 63 optimal weight: 5.9990 overall best weight: 2.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS D 270 ASN D 520 HIS ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.124379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.108062 restraints weight = 75802.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.109284 restraints weight = 141821.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.109871 restraints weight = 79106.602| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 31638 Z= 0.304 Angle : 0.755 18.187 42956 Z= 0.389 Chirality : 0.046 0.211 5051 Planarity : 0.005 0.070 5639 Dihedral : 5.377 26.460 4585 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.78 % Favored : 91.17 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 3985 helix: 0.88 (0.12), residues: 1922 sheet: -1.78 (0.23), residues: 522 loop : -3.08 (0.14), residues: 1541 =============================================================================== Job complete usr+sys time: 7074.49 seconds wall clock time: 129 minutes 22.96 seconds (7762.96 seconds total)