Starting phenix.real_space_refine on Mon Mar 25 07:20:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1s_21514/03_2024/6w1s_21514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1s_21514/03_2024/6w1s_21514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1s_21514/03_2024/6w1s_21514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1s_21514/03_2024/6w1s_21514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1s_21514/03_2024/6w1s_21514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w1s_21514/03_2024/6w1s_21514.pdb" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 154 5.16 5 C 29906 2.51 5 N 8672 2.21 5 O 8543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 87": "NH1" <-> "NH2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I ARG 664": "NH1" <-> "NH2" Residue "I GLU 666": "OE1" <-> "OE2" Residue "I GLU 680": "OE1" <-> "OE2" Residue "I ARG 717": "NH1" <-> "NH2" Residue "I ARG 721": "NH1" <-> "NH2" Residue "I ARG 781": "NH1" <-> "NH2" Residue "I ARG 902": "NH1" <-> "NH2" Residue "I ARG 943": "NH1" <-> "NH2" Residue "J ARG 672": "NH1" <-> "NH2" Residue "K ARG 30": "NH1" <-> "NH2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "K GLU 492": "OE1" <-> "OE2" Residue "K ARG 634": "NH1" <-> "NH2" Residue "K ARG 741": "NH1" <-> "NH2" Residue "L GLU 294": "OE1" <-> "OE2" Residue "L ARG 501": "NH1" <-> "NH2" Residue "L ARG 617": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "R GLU 88": "OE1" <-> "OE2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R ARG 620": "NH1" <-> "NH2" Residue "R GLU 679": "OE1" <-> "OE2" Residue "R GLU 763": "OE1" <-> "OE2" Residue "R ARG 813": "NH1" <-> "NH2" Residue "R GLU 910": "OE1" <-> "OE2" Residue "R ARG 962": "NH1" <-> "NH2" Residue "R GLU 976": "OE1" <-> "OE2" Residue "R ARG 1074": "NH1" <-> "NH2" Residue "R ARG 1139": "NH1" <-> "NH2" Residue "R PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 1315": "OE1" <-> "OE2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S ARG 133": "NH1" <-> "NH2" Residue "S ARG 389": "NH1" <-> "NH2" Residue "S GLU 534": "OE1" <-> "OE2" Residue "S ARG 642": "NH1" <-> "NH2" Residue "S ARG 833": "NH1" <-> "NH2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "T ARG 176": "NH1" <-> "NH2" Residue "T ARG 186": "NH1" <-> "NH2" Residue "T ARG 192": "NH1" <-> "NH2" Residue "V ARG 48": "NH1" <-> "NH2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W ARG 137": "NH1" <-> "NH2" Residue "X GLU 107": "OE1" <-> "OE2" Residue "Y ARG 56": "NH1" <-> "NH2" Residue "Y ARG 83": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47275 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 1905 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 381} Link IDs: {'CIS': 2, 'TRANS': 378} Chain breaks: 24 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 1143 Unresolved non-hydrogen dihedrals: 381 Planarities with less than four sites: {'UNK:plan-1': 381} Unresolved non-hydrogen planarities: 381 Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 468 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 168 Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 744 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 138} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "D" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 781 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 12, 'TRANS': 144} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 712 Unresolved non-hydrogen dihedrals: 473 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 309 Chain: "E" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 837 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 10, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 246 Chain: "F" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 339 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 122 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 350 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'UNK:plan-1': 70} Unresolved non-hydrogen planarities: 70 Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 578 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 136 Chain: "I" Number of atoms: 6731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 6731 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 594} Link IDs: {'CIS': 1, 'PTRANS': 63, 'TRANS': 1012} Chain breaks: 22 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1809 Unresolved non-hydrogen angles: 2326 Unresolved non-hydrogen dihedrals: 1367 Unresolved non-hydrogen chiralities: 196 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 7, 'UNK:plan-1': 89, 'TYR:plan': 5, 'ASN:plan1': 33, 'TRP:plan': 1, 'ASP:plan': 30, 'PHE:plan': 15, 'GLU:plan': 36, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 857 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1171 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 17, 'TRANS': 149} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "K" Number of atoms: 5070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5070 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 696} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 798 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 22, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 25, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 313 Chain: "L" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3243 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 288} Link IDs: {'PTRANS': 20, 'TRANS': 503} Chain breaks: 10 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 927 Unresolved non-hydrogen angles: 1146 Unresolved non-hydrogen dihedrals: 734 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 36, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 16, 'ASP:plan': 19, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 478 Chain: "M" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1140 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "N" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1013 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 169 Chain: "P" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 523 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 164 Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 754 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 173 Chain: "R" Number of atoms: 9744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 9744 Classifications: {'peptide': 1295} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'CIS': 4, 'PTRANS': 68, 'TRANS': 1222} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 743 Unresolved non-hydrogen angles: 932 Unresolved non-hydrogen dihedrals: 606 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 25, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 388 Chain: "S" Number of atoms: 5875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 5875 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 397} Link IDs: {'PTRANS': 35, 'TRANS': 865} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1213 Unresolved non-hydrogen angles: 1510 Unresolved non-hydrogen dihedrals: 942 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 19, 'ASP:plan': 28, 'PHE:plan': 1, 'GLU:plan': 42, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 535 Chain: "T" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1299 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 15, 'TRANS': 176} Chain breaks: 3 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "V" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1657 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 3 Unresolved non-hydrogen bonds: 477 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 242 Chain: "W" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 773 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Chain: "X" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 839 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "Y" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 843 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 8, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "Z" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 463 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 88} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 246 Time building chain proxies: 25.30, per 1000 atoms: 0.54 Number of scatterers: 47275 At special positions: 0 Unit cell: (157.62, 222, 386.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 154 16.00 O 8543 8.00 N 8672 7.00 C 29906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS O 75 " - pdb=" SG CYS O 84 " distance=2.04 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 161 " distance=2.03 Simple disulfide: pdb=" SG CYS W 55 " - pdb=" SG CYS W 80 " distance=2.03 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: 19.72 Conformation dependent library (CDL) restraints added in 10.4 seconds 13360 Ramachandran restraints generated. 6680 Oldfield, 0 Emsley, 6680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14278 Finding SS restraints... Secondary structure from input PDB file: 282 helices and 27 sheets defined 58.7% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 1800 through 1815 Processing helix chain 'A' and resid 1819 through 1831 Processing helix chain 'A' and resid 1841 through 1857 Processing helix chain 'A' and resid 1862 through 1873 Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 3.838A pdb=" N UNK A1930 " --> pdb=" O UNK A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1947 removed outlier: 3.714A pdb=" N UNK A1942 " --> pdb=" O UNK A1938 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK A1943 " --> pdb=" O UNK A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1979 removed outlier: 3.568A pdb=" N UNK A1978 " --> pdb=" O UNK A1974 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N UNK A1979 " --> pdb=" O UNK A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2205 Processing helix chain 'A' and resid 2227 through 2239 Processing helix chain 'A' and resid 2316 through 2324 Processing helix chain 'A' and resid 2339 through 2349 Processing helix chain 'A' and resid 2400 through 2422 removed outlier: 3.753A pdb=" N UNK A2404 " --> pdb=" O UNK A2400 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N UNK A2405 " --> pdb=" O UNK A2401 " (cutoff:3.500A) Processing helix chain 'A' and resid 2491 through 2513 Processing helix chain 'A' and resid 2616 through 2628 Processing helix chain 'A' and resid 2661 through 2667 removed outlier: 3.933A pdb=" N UNK A2665 " --> pdb=" O UNK A2661 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 59 through 129 removed outlier: 4.057A pdb=" N LYS B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 4.084A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.973A pdb=" N VAL C 49 " --> pdb=" O CYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.663A pdb=" N LEU C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.958A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'D' and resid 73 through 99 removed outlier: 3.673A pdb=" N GLU D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 167 Proline residue: D 128 - end of helix removed outlier: 3.833A pdb=" N CYS D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 33 Processing helix chain 'E' and resid 44 through 66 removed outlier: 4.212A pdb=" N GLU E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.632A pdb=" N GLN E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.865A pdb=" N SER E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 127 removed outlier: 4.401A pdb=" N ASP E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 163 Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.895A pdb=" N THR E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 74 Processing helix chain 'F' and resid 82 through 98 removed outlier: 3.588A pdb=" N GLY F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 removed outlier: 3.789A pdb=" N TYR F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 209 Processing helix chain 'G' and resid 214 through 236 Processing helix chain 'G' and resid 239 through 255 Processing helix chain 'G' and resid 258 through 268 Processing helix chain 'H' and resid 9 through 38 removed outlier: 4.268A pdb=" N GLU H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 68 Processing helix chain 'H' and resid 83 through 115 Processing helix chain 'I' and resid 154 through 167 removed outlier: 3.559A pdb=" N ALA I 159 " --> pdb=" O LEU I 155 " (cutoff:3.500A) Proline residue: I 161 - end of helix removed outlier: 3.913A pdb=" N LEU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 212 Processing helix chain 'I' and resid 277 through 287 Processing helix chain 'I' and resid 293 through 324 removed outlier: 5.017A pdb=" N LEU I 302 " --> pdb=" O MET I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 430 removed outlier: 4.236A pdb=" N LEU I 407 " --> pdb=" O ILE I 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 492 removed outlier: 3.758A pdb=" N SER I 487 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 516 removed outlier: 3.650A pdb=" N CYS I 511 " --> pdb=" O GLY I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 601 through 609 Processing helix chain 'I' and resid 643 through 668 removed outlier: 3.648A pdb=" N LEU I 647 " --> pdb=" O PHE I 643 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS I 649 " --> pdb=" O LYS I 645 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS I 654 " --> pdb=" O PHE I 650 " (cutoff:3.500A) Proline residue: I 659 - end of helix removed outlier: 3.952A pdb=" N GLU I 666 " --> pdb=" O GLY I 662 " (cutoff:3.500A) Processing helix chain 'I' and resid 702 through 711 removed outlier: 3.532A pdb=" N ARG I 709 " --> pdb=" O LYS I 705 " (cutoff:3.500A) Processing helix chain 'I' and resid 768 through 790 removed outlier: 3.529A pdb=" N ALA I 790 " --> pdb=" O VAL I 786 " (cutoff:3.500A) Processing helix chain 'I' and resid 795 through 799 Processing helix chain 'I' and resid 857 through 868 Processing helix chain 'I' and resid 870 through 889 removed outlier: 5.049A pdb=" N ALA I 883 " --> pdb=" O PHE I 879 " (cutoff:3.500A) Proline residue: I 884 - end of helix Processing helix chain 'I' and resid 965 through 972 removed outlier: 3.559A pdb=" N LEU I 969 " --> pdb=" O LEU I 965 " (cutoff:3.500A) Processing helix chain 'I' and resid 1181 through 1181 No H-bonds generated for 'chain 'I' and resid 1181 through 1181' Processing helix chain 'I' and resid 1185 through 1191 Processing helix chain 'I' and resid 1210 through 1232 Processing helix chain 'I' and resid 1282 through 1296 removed outlier: 3.960A pdb=" N ALA I1295 " --> pdb=" O GLU I1291 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I1296 " --> pdb=" O THR I1292 " (cutoff:3.500A) Processing helix chain 'I' and resid 1301 through 1310 removed outlier: 3.510A pdb=" N ILE I1305 " --> pdb=" O ALA I1301 " (cutoff:3.500A) Processing helix chain 'I' and resid 1316 through 1328 Processing helix chain 'I' and resid 1412 through 1426 Proline residue: I1417 - end of helix Processing helix chain 'I' and resid 1439 through 1449 Processing helix chain 'I' and resid 2006 through 2022 removed outlier: 3.758A pdb=" N UNK I2020 " --> pdb=" O UNK I2016 " (cutoff:3.500A) Processing helix chain 'I' and resid 2034 through 2074 removed outlier: 3.881A pdb=" N UNK I2074 " --> pdb=" O UNK I2070 " (cutoff:3.500A) Processing helix chain 'I' and resid 2080 through 2096 removed outlier: 4.503A pdb=" N UNK I2085 " --> pdb=" O UNK I2081 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N UNK I2086 " --> pdb=" O UNK I2082 " (cutoff:3.500A) Processing helix chain 'J' and resid 622 through 631 Processing helix chain 'J' and resid 637 through 651 Proline residue: J 645 - end of helix Processing helix chain 'J' and resid 676 through 685 Processing helix chain 'J' and resid 739 through 747 removed outlier: 3.593A pdb=" N TYR J 744 " --> pdb=" O ARG J 740 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP J 745 " --> pdb=" O GLN J 741 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN J 747 " --> pdb=" O GLN J 743 " (cutoff:3.500A) Processing helix chain 'J' and resid 747 through 762 removed outlier: 3.652A pdb=" N CYS J 756 " --> pdb=" O SER J 752 " (cutoff:3.500A) Processing helix chain 'J' and resid 770 through 784 Processing helix chain 'K' and resid 221 through 225 removed outlier: 3.620A pdb=" N SER K 225 " --> pdb=" O SER K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 472 Processing helix chain 'K' and resid 476 through 480 removed outlier: 3.586A pdb=" N LEU K 479 " --> pdb=" O TRP K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 486 Processing helix chain 'K' and resid 487 through 501 Processing helix chain 'K' and resid 504 through 523 removed outlier: 4.223A pdb=" N VAL K 508 " --> pdb=" O ALA K 504 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR K 511 " --> pdb=" O GLN K 507 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG K 512 " --> pdb=" O VAL K 508 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA K 515 " --> pdb=" O THR K 511 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU K 523 " --> pdb=" O SER K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 552 removed outlier: 3.548A pdb=" N LEU K 538 " --> pdb=" O TYR K 534 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE K 539 " --> pdb=" O HIS K 535 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG K 552 " --> pdb=" O LYS K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 563 through 565 No H-bonds generated for 'chain 'K' and resid 563 through 565' Processing helix chain 'K' and resid 566 through 571 Processing helix chain 'K' and resid 578 through 587 removed outlier: 3.550A pdb=" N VAL K 582 " --> pdb=" O ASP K 578 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE K 584 " --> pdb=" O ASP K 580 " (cutoff:3.500A) Processing helix chain 'K' and resid 605 through 618 removed outlier: 4.035A pdb=" N LEU K 613 " --> pdb=" O GLY K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 656 Processing helix chain 'K' and resid 672 through 686 removed outlier: 4.466A pdb=" N CYS K 686 " --> pdb=" O LYS K 682 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 728 removed outlier: 3.620A pdb=" N ARG K 728 " --> pdb=" O GLY K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 803 through 812 removed outlier: 3.925A pdb=" N GLU K 807 " --> pdb=" O VAL K 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS K 812 " --> pdb=" O GLN K 808 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 Processing helix chain 'L' and resid 35 through 47 Processing helix chain 'L' and resid 95 through 118 Processing helix chain 'L' and resid 141 through 175 removed outlier: 3.775A pdb=" N LYS L 148 " --> pdb=" O LEU L 144 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE L 157 " --> pdb=" O GLY L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 192 Processing helix chain 'L' and resid 288 through 314 removed outlier: 4.083A pdb=" N ALA L 295 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA L 296 " --> pdb=" O LYS L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 383 Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 414 through 419 Processing helix chain 'L' and resid 424 through 452 removed outlier: 3.980A pdb=" N LYS L 428 " --> pdb=" O GLY L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 539 removed outlier: 3.690A pdb=" N ASP L 521 " --> pdb=" O GLN L 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 602 through 607 removed outlier: 3.897A pdb=" N ASP L 606 " --> pdb=" O LEU L 602 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL L 607 " --> pdb=" O PRO L 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 602 through 607' Processing helix chain 'L' and resid 633 through 635 No H-bonds generated for 'chain 'L' and resid 633 through 635' Processing helix chain 'L' and resid 636 through 641 Processing helix chain 'M' and resid 32 through 42 removed outlier: 3.899A pdb=" N ARG M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 122 Processing helix chain 'M' and resid 180 through 193 removed outlier: 4.338A pdb=" N ASP M 184 " --> pdb=" O ASP M 180 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP M 185 " --> pdb=" O MET M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 502 through 507 Processing helix chain 'N' and resid 509 through 515 removed outlier: 3.664A pdb=" N UNK N 515 " --> pdb=" O UNK N 511 " (cutoff:3.500A) Processing helix chain 'N' and resid 549 through 558 Processing helix chain 'O' and resid 16 through 32 Processing helix chain 'O' and resid 89 through 98 Processing helix chain 'O' and resid 154 through 163 removed outlier: 3.849A pdb=" N SER O 163 " --> pdb=" O GLU O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 200 removed outlier: 4.320A pdb=" N MET O 190 " --> pdb=" O PRO O 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 26 Processing helix chain 'P' and resid 50 through 75 Processing helix chain 'P' and resid 84 through 128 removed outlier: 3.518A pdb=" N SER P 128 " --> pdb=" O ASP P 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 39 Processing helix chain 'Q' and resid 49 through 89 removed outlier: 4.107A pdb=" N GLU Q 55 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN Q 89 " --> pdb=" O PHE Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 135 removed outlier: 3.814A pdb=" N ASP Q 99 " --> pdb=" O ASN Q 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU Q 133 " --> pdb=" O GLU Q 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 35 through 50 Processing helix chain 'R' and resid 51 through 54 removed outlier: 5.536A pdb=" N GLU R 54 " --> pdb=" O LEU R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 55 through 68 Processing helix chain 'R' and resid 72 through 89 Processing helix chain 'R' and resid 93 through 103 removed outlier: 4.027A pdb=" N ASN R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 125 Processing helix chain 'R' and resid 134 through 147 Processing helix chain 'R' and resid 161 through 174 Processing helix chain 'R' and resid 179 through 187 removed outlier: 3.637A pdb=" N ALA R 183 " --> pdb=" O PRO R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 190 No H-bonds generated for 'chain 'R' and resid 188 through 190' Processing helix chain 'R' and resid 202 through 218 removed outlier: 4.008A pdb=" N SER R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Proline residue: R 214 - end of helix Processing helix chain 'R' and resid 266 through 275 Processing helix chain 'R' and resid 279 through 288 Processing helix chain 'R' and resid 299 through 316 Processing helix chain 'R' and resid 317 through 324 removed outlier: 4.553A pdb=" N PHE R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 342 removed outlier: 4.085A pdb=" N HIS R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU R 338 " --> pdb=" O LEU R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 360 removed outlier: 3.795A pdb=" N SER R 355 " --> pdb=" O HIS R 351 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU R 356 " --> pdb=" O MET R 352 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 384 removed outlier: 4.611A pdb=" N GLY R 382 " --> pdb=" O GLN R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 401 removed outlier: 3.648A pdb=" N PHE R 392 " --> pdb=" O ALA R 388 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 419 through 440 removed outlier: 5.274A pdb=" N MET R 425 " --> pdb=" O HIS R 421 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR R 426 " --> pdb=" O ALA R 422 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP R 429 " --> pdb=" O MET R 425 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY R 439 " --> pdb=" O LYS R 435 " (cutoff:3.500A) Processing helix chain 'R' and resid 441 through 445 Processing helix chain 'R' and resid 448 through 450 No H-bonds generated for 'chain 'R' and resid 448 through 450' Processing helix chain 'R' and resid 451 through 456 removed outlier: 4.005A pdb=" N GLU R 456 " --> pdb=" O LYS R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 474 through 478 removed outlier: 3.586A pdb=" N LEU R 477 " --> pdb=" O ILE R 474 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS R 478 " --> pdb=" O ALA R 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 474 through 478' Processing helix chain 'R' and resid 489 through 494 Processing helix chain 'R' and resid 542 through 554 removed outlier: 3.667A pdb=" N ILE R 548 " --> pdb=" O ALA R 544 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR R 553 " --> pdb=" O LYS R 549 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS R 554 " --> pdb=" O LEU R 550 " (cutoff:3.500A) Processing helix chain 'R' and resid 563 through 569 Processing helix chain 'R' and resid 570 through 577 Processing helix chain 'R' and resid 577 through 589 removed outlier: 3.716A pdb=" N ILE R 581 " --> pdb=" O GLU R 577 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS R 582 " --> pdb=" O SER R 578 " (cutoff:3.500A) Processing helix chain 'R' and resid 590 through 595 Processing helix chain 'R' and resid 600 through 611 removed outlier: 3.744A pdb=" N LEU R 604 " --> pdb=" O ILE R 600 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU R 606 " --> pdb=" O HIS R 602 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET R 607 " --> pdb=" O THR R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 633 removed outlier: 4.215A pdb=" N GLN R 622 " --> pdb=" O HIS R 618 " (cutoff:3.500A) Processing helix chain 'R' and resid 642 through 656 removed outlier: 3.573A pdb=" N GLU R 646 " --> pdb=" O HIS R 642 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA R 655 " --> pdb=" O ARG R 651 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU R 656 " --> pdb=" O LEU R 652 " (cutoff:3.500A) Processing helix chain 'R' and resid 660 through 665 Processing helix chain 'R' and resid 670 through 675 Processing helix chain 'R' and resid 680 through 696 Processing helix chain 'R' and resid 709 through 720 removed outlier: 3.883A pdb=" N ASP R 714 " --> pdb=" O THR R 710 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE R 715 " --> pdb=" O TRP R 711 " (cutoff:3.500A) Processing helix chain 'R' and resid 721 through 723 No H-bonds generated for 'chain 'R' and resid 721 through 723' Processing helix chain 'R' and resid 739 through 748 removed outlier: 4.983A pdb=" N GLN R 745 " --> pdb=" O PHE R 742 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN R 746 " --> pdb=" O PHE R 743 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL R 748 " --> pdb=" O GLN R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 770 removed outlier: 4.038A pdb=" N LYS R 758 " --> pdb=" O PHE R 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 776 through 781 Processing helix chain 'R' and resid 785 through 795 removed outlier: 3.922A pdb=" N PHE R 789 " --> pdb=" O PRO R 786 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU R 790 " --> pdb=" O PRO R 787 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS R 791 " --> pdb=" O LEU R 788 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU R 793 " --> pdb=" O LEU R 790 " (cutoff:3.500A) Processing helix chain 'R' and resid 807 through 812 Processing helix chain 'R' and resid 814 through 836 removed outlier: 4.461A pdb=" N ALA R 818 " --> pdb=" O ILE R 814 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL R 820 " --> pdb=" O ALA R 816 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA R 821 " --> pdb=" O ARG R 817 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR R 825 " --> pdb=" O ALA R 821 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE R 826 " --> pdb=" O HIS R 822 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP R 828 " --> pdb=" O ARG R 824 " (cutoff:3.500A) Processing helix chain 'R' and resid 842 through 855 removed outlier: 3.855A pdb=" N ASN R 851 " --> pdb=" O ILE R 847 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP R 852 " --> pdb=" O GLU R 848 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP R 855 " --> pdb=" O ASN R 851 " (cutoff:3.500A) Processing helix chain 'R' and resid 864 through 872 removed outlier: 3.869A pdb=" N ALA R 870 " --> pdb=" O ILE R 866 " (cutoff:3.500A) Processing helix chain 'R' and resid 878 through 883 Processing helix chain 'R' and resid 884 through 889 Processing helix chain 'R' and resid 896 through 904 removed outlier: 3.874A pdb=" N SER R 901 " --> pdb=" O ARG R 897 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP R 902 " --> pdb=" O ASN R 898 " (cutoff:3.500A) Processing helix chain 'R' and resid 916 through 928 Processing helix chain 'R' and resid 956 through 971 removed outlier: 3.792A pdb=" N LEU R 961 " --> pdb=" O GLY R 957 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG R 962 " --> pdb=" O ASN R 958 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU R 964 " --> pdb=" O CYS R 960 " (cutoff:3.500A) Proline residue: R 965 - end of helix removed outlier: 3.653A pdb=" N ILE R 971 " --> pdb=" O PHE R 967 " (cutoff:3.500A) Processing helix chain 'R' and resid 978 through 981 Processing helix chain 'R' and resid 982 through 991 removed outlier: 4.252A pdb=" N THR R 986 " --> pdb=" O LYS R 982 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU R 987 " --> pdb=" O SER R 983 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP R 989 " --> pdb=" O GLU R 985 " (cutoff:3.500A) Processing helix chain 'R' and resid 992 through 997 removed outlier: 4.024A pdb=" N PHE R 997 " --> pdb=" O LEU R 994 " (cutoff:3.500A) Processing helix chain 'R' and resid 1001 through 1007 Processing helix chain 'R' and resid 1012 through 1015 Processing helix chain 'R' and resid 1016 through 1036 removed outlier: 4.051A pdb=" N LEU R1022 " --> pdb=" O ASN R1018 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS R1025 " --> pdb=" O HIS R1021 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS R1028 " --> pdb=" O ARG R1024 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R1029 " --> pdb=" O LYS R1025 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY R1032 " --> pdb=" O HIS R1028 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER R1033 " --> pdb=" O ALA R1029 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU R1034 " --> pdb=" O ILE R1030 " (cutoff:3.500A) Processing helix chain 'R' and resid 1043 through 1053 removed outlier: 3.764A pdb=" N THR R1047 " --> pdb=" O CYS R1043 " (cutoff:3.500A) Processing helix chain 'R' and resid 1058 through 1062 removed outlier: 3.684A pdb=" N TRP R1061 " --> pdb=" O ASP R1058 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL R1062 " --> pdb=" O ASN R1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1058 through 1062' Processing helix chain 'R' and resid 1063 through 1077 removed outlier: 3.872A pdb=" N LEU R1075 " --> pdb=" O LEU R1071 " (cutoff:3.500A) Processing helix chain 'R' and resid 1102 through 1114 removed outlier: 4.290A pdb=" N HIS R1106 " --> pdb=" O ALA R1102 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL R1107 " --> pdb=" O HIS R1103 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR R1108 " --> pdb=" O ALA R1104 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU R1112 " --> pdb=" O THR R1108 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA R1114 " --> pdb=" O VAL R1110 " (cutoff:3.500A) Processing helix chain 'R' and resid 1120 through 1128 removed outlier: 3.666A pdb=" N ASN R1124 " --> pdb=" O LYS R1120 " (cutoff:3.500A) Processing helix chain 'R' and resid 1141 through 1154 Processing helix chain 'R' and resid 1157 through 1162 removed outlier: 3.624A pdb=" N TRP R1161 " --> pdb=" O PRO R1157 " (cutoff:3.500A) Processing helix chain 'R' and resid 1162 through 1171 removed outlier: 4.129A pdb=" N ASP R1166 " --> pdb=" O ILE R1162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL R1171 " --> pdb=" O ARG R1167 " (cutoff:3.500A) Processing helix chain 'R' and resid 1172 through 1175 removed outlier: 3.786A pdb=" N SER R1175 " --> pdb=" O ILE R1172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1172 through 1175' Processing helix chain 'R' and resid 1182 through 1185 Processing helix chain 'R' and resid 1186 through 1192 removed outlier: 3.974A pdb=" N LEU R1190 " --> pdb=" O TYR R1186 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP R1192 " --> pdb=" O PHE R1188 " (cutoff:3.500A) Processing helix chain 'R' and resid 1203 through 1219 removed outlier: 3.557A pdb=" N TYR R1207 " --> pdb=" O MET R1203 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR R1208 " --> pdb=" O SER R1204 " (cutoff:3.500A) Processing helix chain 'R' and resid 1222 through 1225 Processing helix chain 'R' and resid 1226 through 1235 Processing helix chain 'R' and resid 1236 through 1239 Processing helix chain 'R' and resid 1241 through 1253 removed outlier: 4.028A pdb=" N LEU R1245 " --> pdb=" O THR R1241 " (cutoff:3.500A) Processing helix chain 'R' and resid 1255 through 1263 removed outlier: 4.270A pdb=" N GLU R1262 " --> pdb=" O ARG R1258 " (cutoff:3.500A) Processing helix chain 'R' and resid 1265 through 1284 removed outlier: 4.059A pdb=" N GLU R1269 " --> pdb=" O ARG R1265 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS R1284 " --> pdb=" O ASN R1280 " (cutoff:3.500A) Processing helix chain 'R' and resid 1291 through 1305 removed outlier: 3.750A pdb=" N ASP R1296 " --> pdb=" O ASP R1292 " (cutoff:3.500A) Processing helix chain 'R' and resid 1310 through 1319 removed outlier: 4.678A pdb=" N LYS R1316 " --> pdb=" O GLU R1312 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE R1317 " --> pdb=" O GLN R1313 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N CYS R1319 " --> pdb=" O GLU R1315 " (cutoff:3.500A) Processing helix chain 'R' and resid 1322 through 1329 Processing helix chain 'R' and resid 1330 through 1334 Processing helix chain 'S' and resid 5 through 16 Processing helix chain 'S' and resid 21 through 31 removed outlier: 3.881A pdb=" N ILE S 25 " --> pdb=" O TYR S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 42 No H-bonds generated for 'chain 'S' and resid 40 through 42' Processing helix chain 'S' and resid 43 through 53 removed outlier: 4.461A pdb=" N LEU S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU S 48 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 69 Processing helix chain 'S' and resid 72 through 83 removed outlier: 3.966A pdb=" N SER S 76 " --> pdb=" O MET S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 89 Processing helix chain 'S' and resid 92 through 108 removed outlier: 3.890A pdb=" N ASP S 99 " --> pdb=" O GLN S 95 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET S 103 " --> pdb=" O ASP S 99 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE S 104 " --> pdb=" O ILE S 100 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS S 105 " --> pdb=" O MET S 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG S 107 " --> pdb=" O MET S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 139 Processing helix chain 'S' and resid 156 through 169 removed outlier: 4.025A pdb=" N LEU S 162 " --> pdb=" O LEU S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 185 Processing helix chain 'S' and resid 186 through 204 removed outlier: 3.631A pdb=" N ILE S 202 " --> pdb=" O LYS S 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA S 204 " --> pdb=" O GLY S 200 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 228 removed outlier: 3.856A pdb=" N ARG S 217 " --> pdb=" O SER S 213 " (cutoff:3.500A) Proline residue: S 226 - end of helix Processing helix chain 'S' and resid 241 through 254 removed outlier: 3.770A pdb=" N HIS S 245 " --> pdb=" O PHE S 241 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU S 249 " --> pdb=" O HIS S 245 " (cutoff:3.500A) Processing helix chain 'S' and resid 261 through 273 removed outlier: 3.516A pdb=" N MET S 273 " --> pdb=" O MET S 269 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 292 removed outlier: 3.698A pdb=" N GLY S 292 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 323 removed outlier: 3.731A pdb=" N ALA S 307 " --> pdb=" O LEU S 303 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE S 313 " --> pdb=" O THR S 309 " (cutoff:3.500A) Proline residue: S 314 - end of helix Processing helix chain 'S' and resid 331 through 343 removed outlier: 3.995A pdb=" N ASN S 335 " --> pdb=" O THR S 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 344 through 356 removed outlier: 3.930A pdb=" N LEU S 348 " --> pdb=" O LEU S 344 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS S 355 " --> pdb=" O ALA S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 369 removed outlier: 3.557A pdb=" N ASN S 361 " --> pdb=" O CYS S 357 " (cutoff:3.500A) Processing helix chain 'S' and resid 370 through 372 No H-bonds generated for 'chain 'S' and resid 370 through 372' Processing helix chain 'S' and resid 377 through 388 Processing helix chain 'S' and resid 411 through 420 Processing helix chain 'S' and resid 421 through 426 removed outlier: 3.549A pdb=" N HIS S 426 " --> pdb=" O ASP S 423 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 444 removed outlier: 4.001A pdb=" N HIS S 439 " --> pdb=" O GLY S 435 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER S 442 " --> pdb=" O GLY S 438 " (cutoff:3.500A) Processing helix chain 'S' and resid 447 through 455 removed outlier: 3.958A pdb=" N ALA S 451 " --> pdb=" O ASP S 447 " (cutoff:3.500A) Processing helix chain 'S' and resid 458 through 473 removed outlier: 3.633A pdb=" N ASN S 470 " --> pdb=" O PHE S 466 " (cutoff:3.500A) Processing helix chain 'S' and resid 480 through 505 Processing helix chain 'S' and resid 506 through 514 Processing helix chain 'S' and resid 523 through 528 Processing helix chain 'S' and resid 551 through 562 removed outlier: 3.875A pdb=" N SER S 562 " --> pdb=" O LEU S 558 " (cutoff:3.500A) Processing helix chain 'S' and resid 577 through 591 removed outlier: 3.730A pdb=" N ALA S 581 " --> pdb=" O LEU S 577 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU S 587 " --> pdb=" O ILE S 583 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN S 588 " --> pdb=" O LEU S 584 " (cutoff:3.500A) Processing helix chain 'S' and resid 597 through 607 removed outlier: 3.588A pdb=" N THR S 604 " --> pdb=" O ILE S 600 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP S 605 " --> pdb=" O GLN S 601 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN S 606 " --> pdb=" O LYS S 602 " (cutoff:3.500A) Processing helix chain 'S' and resid 613 through 628 Processing helix chain 'S' and resid 633 through 644 removed outlier: 3.749A pdb=" N SER S 637 " --> pdb=" O GLU S 633 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU S 638 " --> pdb=" O ARG S 634 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE S 641 " --> pdb=" O SER S 637 " (cutoff:3.500A) Processing helix chain 'S' and resid 659 through 672 removed outlier: 3.615A pdb=" N CYS S 672 " --> pdb=" O LEU S 668 " (cutoff:3.500A) Processing helix chain 'S' and resid 673 through 679 removed outlier: 3.658A pdb=" N GLN S 677 " --> pdb=" O ALA S 673 " (cutoff:3.500A) Processing helix chain 'S' and resid 711 through 717 Processing helix chain 'S' and resid 725 through 737 removed outlier: 4.114A pdb=" N ILE S 729 " --> pdb=" O ARG S 725 " (cutoff:3.500A) Processing helix chain 'S' and resid 738 through 751 Processing helix chain 'S' and resid 755 through 770 removed outlier: 3.943A pdb=" N SER S 768 " --> pdb=" O GLN S 764 " (cutoff:3.500A) Processing helix chain 'S' and resid 773 through 792 Proline residue: S 787 - end of helix removed outlier: 3.557A pdb=" N ASP S 792 " --> pdb=" O GLY S 788 " (cutoff:3.500A) Processing helix chain 'S' and resid 793 through 800 removed outlier: 3.945A pdb=" N HIS S 797 " --> pdb=" O SER S 793 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER S 798 " --> pdb=" O SER S 794 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU S 799 " --> pdb=" O LYS S 795 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET S 800 " --> pdb=" O TRP S 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 793 through 800' Processing helix chain 'S' and resid 802 through 820 removed outlier: 3.563A pdb=" N ALA S 806 " --> pdb=" O PRO S 802 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER S 820 " --> pdb=" O LEU S 816 " (cutoff:3.500A) Processing helix chain 'S' and resid 828 through 833 removed outlier: 4.024A pdb=" N LYS S 832 " --> pdb=" O SER S 828 " (cutoff:3.500A) Processing helix chain 'S' and resid 893 through 910 Processing helix chain 'S' and resid 916 through 930 removed outlier: 3.854A pdb=" N GLN S 920 " --> pdb=" O GLY S 916 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL S 922 " --> pdb=" O HIS S 918 " (cutoff:3.500A) Processing helix chain 'S' and resid 944 through 956 removed outlier: 4.451A pdb=" N THR S 948 " --> pdb=" O PHE S 944 " (cutoff:3.500A) Processing helix chain 'S' and resid 962 through 967 removed outlier: 4.284A pdb=" N ALA S 967 " --> pdb=" O LYS S 963 " (cutoff:3.500A) Processing helix chain 'S' and resid 973 through 985 removed outlier: 3.896A pdb=" N ARG S 977 " --> pdb=" O LEU S 973 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN S 978 " --> pdb=" O PRO S 974 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL S 979 " --> pdb=" O LEU S 975 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 44 removed outlier: 4.220A pdb=" N GLU T 34 " --> pdb=" O PRO T 30 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS T 38 " --> pdb=" O GLU T 34 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU T 41 " --> pdb=" O LYS T 37 " (cutoff:3.500A) Proline residue: T 42 - end of helix Processing helix chain 'T' and resid 88 through 91 removed outlier: 4.497A pdb=" N ALA T 91 " --> pdb=" O THR T 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 88 through 91' Processing helix chain 'T' and resid 92 through 99 removed outlier: 3.714A pdb=" N ASP T 99 " --> pdb=" O VAL T 95 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 132 removed outlier: 3.631A pdb=" N THR T 120 " --> pdb=" O GLU T 116 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA T 121 " --> pdb=" O GLY T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 Processing helix chain 'T' and resid 189 through 196 removed outlier: 4.582A pdb=" N LEU T 193 " --> pdb=" O PRO T 189 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU T 194 " --> pdb=" O ALA T 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 35 removed outlier: 3.802A pdb=" N ALA V 13 " --> pdb=" O VAL V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 72 removed outlier: 3.802A pdb=" N ALA V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU V 71 " --> pdb=" O LEU V 67 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG V 72 " --> pdb=" O ASN V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 129 Processing helix chain 'V' and resid 161 through 172 removed outlier: 4.035A pdb=" N VAL V 165 " --> pdb=" O TYR V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 251 Processing helix chain 'V' and resid 258 through 271 Processing helix chain 'V' and resid 272 through 275 removed outlier: 4.249A pdb=" N LYS V 275 " --> pdb=" O SER V 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 272 through 275' Processing helix chain 'W' and resid 45 through 55 Processing helix chain 'W' and resid 72 through 106 removed outlier: 3.699A pdb=" N GLN W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS W 83 " --> pdb=" O GLN W 79 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE W 84 " --> pdb=" O CYS W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 147 removed outlier: 4.199A pdb=" N VAL W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 89 Proline residue: X 64 - end of helix Processing helix chain 'X' and resid 101 through 134 removed outlier: 3.526A pdb=" N LEU X 105 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU X 107 " --> pdb=" O LYS X 103 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER X 132 " --> pdb=" O GLN X 128 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS X 134 " --> pdb=" O CYS X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 185 removed outlier: 3.958A pdb=" N THR X 185 " --> pdb=" O ALA X 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 57 removed outlier: 3.704A pdb=" N ASN Y 57 " --> pdb=" O GLN Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 102 Processing helix chain 'Y' and resid 109 through 113 removed outlier: 4.511A pdb=" N GLU Y 112 " --> pdb=" O ILE Y 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 174 removed outlier: 3.624A pdb=" N GLN Y 162 " --> pdb=" O GLN Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 177 No H-bonds generated for 'chain 'Y' and resid 175 through 177' Processing helix chain 'Z' and resid 15 through 29 Processing helix chain 'Z' and resid 31 through 41 removed outlier: 4.210A pdb=" N ASN Z 35 " --> pdb=" O PRO Z 31 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE Z 36 " --> pdb=" O ASN Z 32 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY Z 41 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 44 No H-bonds generated for 'chain 'Z' and resid 42 through 44' Processing helix chain 'Z' and resid 45 through 56 removed outlier: 3.978A pdb=" N VAL Z 49 " --> pdb=" O ASP Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 57 through 60 removed outlier: 4.448A pdb=" N GLU Z 60 " --> pdb=" O TYR Z 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 57 through 60' Processing helix chain 'Z' and resid 71 through 79 Processing helix chain 'Z' and resid 81 through 90 removed outlier: 3.640A pdb=" N ASN Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 105 removed outlier: 3.714A pdb=" N ALA Z 94 " --> pdb=" O ASN Z 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2362 through 2364 removed outlier: 3.709A pdb=" N UNK A2374 " --> pdb=" O UNK A2364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 69 through 72 removed outlier: 4.243A pdb=" N LEU C 70 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG C 82 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'I' and resid 228 through 229 Processing sheet with id=AA5, first strand: chain 'I' and resid 332 through 333 Processing sheet with id=AA6, first strand: chain 'I' and resid 438 through 439 removed outlier: 3.500A pdb=" N GLU I 438 " --> pdb=" O ILE I 445 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU I 444 " --> pdb=" O ILE I 460 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE I 460 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS I 459 " --> pdb=" O MET I 472 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 522 through 523 Processing sheet with id=AA8, first strand: chain 'I' and resid 688 through 690 removed outlier: 3.815A pdb=" N ILE I 688 " --> pdb=" O PHE I 716 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 690 " --> pdb=" O CYS I 714 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS I 714 " --> pdb=" O LEU I 690 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL I 727 " --> pdb=" O ARG I 717 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 813 through 815 removed outlier: 3.578A pdb=" N ILE I 815 " --> pdb=" O ILE I 826 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN I 829 " --> pdb=" O HIS I 838 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS I 838 " --> pdb=" O GLN I 829 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 930 through 934 Processing sheet with id=AB2, first strand: chain 'K' and resid 50 through 52 Processing sheet with id=AB3, first strand: chain 'K' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'K' and resid 230 through 231 Processing sheet with id=AB5, first strand: chain 'K' and resid 294 through 297 removed outlier: 3.683A pdb=" N VAL K 294 " --> pdb=" O THR K 333 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS K 296 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER K 331 " --> pdb=" O CYS K 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 301 through 302 removed outlier: 3.773A pdb=" N ILE K 324 " --> pdb=" O GLU K 302 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 339 through 340 Processing sheet with id=AB8, first strand: chain 'K' and resid 786 through 787 Processing sheet with id=AB9, first strand: chain 'L' and resid 255 through 256 removed outlier: 3.858A pdb=" N ILE L 341 " --> pdb=" O ILE L 329 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE L 329 " --> pdb=" O ILE L 341 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 459 through 462 Processing sheet with id=AC2, first strand: chain 'L' and resid 501 through 503 Processing sheet with id=AC3, first strand: chain 'L' and resid 569 through 571 removed outlier: 3.670A pdb=" N ILE L 590 " --> pdb=" O ARG L 581 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AC5, first strand: chain 'M' and resid 26 through 28 removed outlier: 3.511A pdb=" N TYR M 167 " --> pdb=" O VAL M 27 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER M 166 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE M 148 " --> pdb=" O SER M 166 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL M 130 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N MET M 125 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU M 59 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS M 127 " --> pdb=" O VAL M 57 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY M 133 " --> pdb=" O PHE M 51 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU M 49 " --> pdb=" O LEU M 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 85 through 87 removed outlier: 3.652A pdb=" N CYS M 105 " --> pdb=" O TYR M 87 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 34 through 35 removed outlier: 4.156A pdb=" N GLU O 34 " --> pdb=" O GLN O 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 66 through 70 removed outlier: 3.792A pdb=" N LEU T 143 " --> pdb=" O VAL T 19 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS T 142 " --> pdb=" O HIS T 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 200 through 202 2745 hydrogen bonds defined for protein. 8058 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: 19.71 Time building geometry restraints manager: 21.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 47865 1.57 - 1.93: 227 1.93 - 2.29: 0 2.29 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 48093 Sorted by residual: bond pdb=" C ALA K 286 " pdb=" N THR K 290 " ideal model delta sigma weight residual 1.329 2.998 -1.669 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C PHE R 250 " pdb=" N PRO R 251 " ideal model delta sigma weight residual 1.331 1.365 -0.034 1.21e-02 6.83e+03 7.74e+00 bond pdb=" C PRO S 802 " pdb=" N PRO S 803 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.44e-02 4.82e+03 3.21e+00 bond pdb=" N GLU R1182 " pdb=" CA GLU R1182 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.73e+00 bond pdb=" C ARG K 627 " pdb=" N PRO K 628 " ideal model delta sigma weight residual 1.332 1.345 -0.013 8.20e-03 1.49e+04 2.37e+00 ... (remaining 48088 not shown) Histogram of bond angle deviations from ideal: 48.57 - 71.83: 1 71.83 - 95.09: 0 95.09 - 118.34: 37490 118.34 - 141.60: 28644 141.60 - 164.86: 2 Bond angle restraints: 66137 Sorted by residual: angle pdb=" O ALA K 286 " pdb=" C ALA K 286 " pdb=" N THR K 290 " ideal model delta sigma weight residual 122.59 48.57 74.02 1.33e+00 5.65e-01 3.10e+03 angle pdb=" CA ALA K 286 " pdb=" C ALA K 286 " pdb=" N THR K 290 " ideal model delta sigma weight residual 116.84 164.86 -48.02 1.71e+00 3.42e-01 7.89e+02 angle pdb=" C ALA K 286 " pdb=" N THR K 290 " pdb=" CA THR K 290 " ideal model delta sigma weight residual 121.70 152.14 -30.44 1.80e+00 3.09e-01 2.86e+02 angle pdb=" N ILE R 947 " pdb=" CA ILE R 947 " pdb=" C ILE R 947 " ideal model delta sigma weight residual 113.53 106.95 6.58 9.80e-01 1.04e+00 4.51e+01 angle pdb=" N HIS K 436 " pdb=" CA HIS K 436 " pdb=" C HIS K 436 " ideal model delta sigma weight residual 114.39 106.15 8.24 1.45e+00 4.76e-01 3.23e+01 ... (remaining 66132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.31: 27132 23.31 - 46.62: 1021 46.62 - 69.94: 77 69.94 - 93.25: 17 93.25 - 116.56: 1 Dihedral angle restraints: 28248 sinusoidal: 6532 harmonic: 21716 Sorted by residual: dihedral pdb=" CA MET D 44 " pdb=" C MET D 44 " pdb=" N PHE D 45 " pdb=" CA PHE D 45 " ideal model delta harmonic sigma weight residual 180.00 63.44 116.56 0 5.00e+00 4.00e-02 5.43e+02 dihedral pdb=" CB CYS S 134 " pdb=" SG CYS S 134 " pdb=" SG CYS S 161 " pdb=" CB CYS S 161 " ideal model delta sinusoidal sigma weight residual 93.00 168.20 -75.20 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CA THR R1181 " pdb=" C THR R1181 " pdb=" N GLU R1182 " pdb=" CA GLU R1182 " ideal model delta harmonic sigma weight residual 180.00 139.61 40.39 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 28245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5918 0.039 - 0.077: 1706 0.077 - 0.116: 469 0.116 - 0.155: 52 0.155 - 0.194: 10 Chirality restraints: 8155 Sorted by residual: chirality pdb=" CA ASP V 95 " pdb=" N ASP V 95 " pdb=" C ASP V 95 " pdb=" CB ASP V 95 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA PRO V 96 " pdb=" N PRO V 96 " pdb=" C PRO V 96 " pdb=" CB PRO V 96 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB ILE K 206 " pdb=" CA ILE K 206 " pdb=" CG1 ILE K 206 " pdb=" CG2 ILE K 206 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 8152 not shown) Planarity restraints: 8766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA K 286 " -0.101 2.00e-02 2.50e+03 8.87e-02 7.88e+01 pdb=" C ALA K 286 " 0.133 2.00e-02 2.50e+03 pdb=" O ALA K 286 " 0.025 2.00e-02 2.50e+03 pdb=" N THR K 290 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP V 95 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO V 96 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO V 96 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO V 96 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER V 93 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C SER V 93 " 0.048 2.00e-02 2.50e+03 pdb=" O SER V 93 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU V 94 " -0.016 2.00e-02 2.50e+03 ... (remaining 8763 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 11 2.04 - 2.76: 8247 2.76 - 3.47: 68511 3.47 - 4.19: 94906 4.19 - 4.90: 165810 Nonbonded interactions: 337485 Sorted by model distance: nonbonded pdb=" N LEU I 150 " pdb=" C UNK I2097 " model vdw 1.330 3.350 nonbonded pdb=" CD2 LEU K 175 " pdb=" CG1 VAL K 201 " model vdw 1.820 3.880 nonbonded pdb=" CD1 LEU K 102 " pdb=" O ARG K 822 " model vdw 1.823 3.460 nonbonded pdb=" CD1 LEU K 102 " pdb=" N ARG K 822 " model vdw 1.829 3.540 nonbonded pdb=" CD2 LEU K 271 " pdb=" CA SER K 279 " model vdw 1.839 3.890 ... (remaining 337480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 8.570 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: 0.050 Extract box with map and model: 40.560 Check model and map are aligned: 0.800 Set scattering table: 0.440 Process input model: 126.610 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 : 0.008 1.669 48093 Z= 0.664 Angle : 0.792 74.024 66137 Z= 0.477 Chirality : 0.040 0.194 8155 Planarity : 0.004 0.110 8766 Dihedral : 12.393 116.559 13961 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.41 % Favored : 86.42 % Rotamer: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.11 % Twisted Proline : 0.91 % Twisted General : 0.12 % 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: -3.32 (0.10), residues: 6680 helix: -0.13 (0.09), residues: 3270 sheet: -3.82 (0.22), residues: 375 loop : -4.57 (0.09), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP T 97 HIS 0.009 0.001 HIS S 735 PHE 0.017 0.001 PHE R 826 TYR 0.018 0.001 TYR R 883 ARG 0.005 0.000 ARG S 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13360 Ramachandran restraints generated. 6680 Oldfield, 0 Emsley, 6680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13360 Ramachandran restraints generated. 6680 Oldfield, 0 Emsley, 6680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 645 time to evaluate : 5.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 293 LYS cc_start: 0.8336 (tptt) cc_final: 0.7891 (tptp) REVERT: I 485 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7347 (mt-10) REVERT: I 970 ASN cc_start: 0.8533 (m-40) cc_final: 0.8300 (m110) REVERT: I 1220 ILE cc_start: 0.8892 (pt) cc_final: 0.8651 (tt) REVERT: K 230 TYR cc_start: 0.8260 (m-10) cc_final: 0.8045 (m-10) REVERT: K 621 ASN cc_start: 0.8535 (m110) cc_final: 0.8290 (t0) REVERT: L 637 MET cc_start: 0.8802 (ppp) cc_final: 0.8384 (ppp) REVERT: M 35 LEU cc_start: 0.8737 (mm) cc_final: 0.8231 (mt) REVERT: M 132 LYS cc_start: 0.7622 (tmtt) cc_final: 0.7418 (tmtt) REVERT: R 285 ASN cc_start: 0.9111 (t0) cc_final: 0.8645 (t0) REVERT: R 574 MET cc_start: 0.1893 (mpp) cc_final: -0.0638 (tpp) REVERT: R 607 MET cc_start: 0.7390 (mmt) cc_final: 0.6825 (mmm) REVERT: R 874 HIS cc_start: 0.6319 (m170) cc_final: 0.6086 (m170) REVERT: R 1291 MET cc_start: 0.7632 (ppp) cc_final: 0.7339 (ppp) REVERT: S 166 GLU cc_start: 0.8787 (tp30) cc_final: 0.8192 (tp30) REVERT: T 45 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7418 (mm-30) REVERT: T 98 LEU cc_start: 0.8852 (tp) cc_final: 0.8620 (tt) REVERT: T 195 PHE cc_start: 0.8316 (m-80) cc_final: 0.8052 (m-80) REVERT: X 61 MET cc_start: 0.8741 (mpp) cc_final: 0.7905 (mmt) REVERT: X 65 GLN cc_start: 0.9009 (mp10) cc_final: 0.8500 (mp10) REVERT: X 106 GLU cc_start: 0.8962 (tp30) cc_final: 0.8503 (tp30) REVERT: Y 74 ARG cc_start: 0.8551 (mtt90) cc_final: 0.8328 (mtt-85) REVERT: Y 91 LYS cc_start: 0.9285 (tttp) cc_final: 0.9071 (ttpt) outliers start: 1 outliers final: 0 residues processed: 646 average time/residue: 0.5758 time to fit residues: 619.9517 Evaluate side-chains 426 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 5.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 618 optimal weight: 8.9990 chunk 554 optimal weight: 0.0770 chunk 307 optimal weight: 10.0000 chunk 189 optimal weight: 0.5980 chunk 374 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 573 optimal weight: 20.0000 chunk 222 optimal weight: 1.9990 chunk 348 optimal weight: 0.2980 chunk 427 optimal weight: 4.9990 chunk 664 optimal weight: 20.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 282 GLN I 317 GLN I 649 HIS I 866 ASN ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 HIS K 270 HIS K 375 GLN ** K 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 HIS K 630 HIS L 371 HIS L 526 GLN M 54 HIS R 614 HIS R 618 HIS R 670 ASN R 684 ASN ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 802 HIS R 851 ASN R 918 HIS ** R1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 GLN S 71 GLN S 111 HIS S 470 ASN S 728 HIS T 209 GLN V 41 ASN V 55 ASN V 109 GLN Y 79 GLN Y 155 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48093 Z= 0.189 Angle : 0.631 20.369 66137 Z= 0.319 Chirality : 0.040 0.286 8155 Planarity : 0.004 0.068 8766 Dihedral : 4.812 58.203 7613 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.75 % Favored : 86.11 % Rotamer: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.11 % Twisted Proline : 0.60 % Twisted General : 0.16 % 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: -2.19 (0.10), residues: 6682 helix: 0.96 (0.09), residues: 3323 sheet: -3.34 (0.23), residues: 389 loop : -4.30 (0.10), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 97 HIS 0.014 0.001 HIS R1197 PHE 0.046 0.001 PHE S 340 TYR 0.018 0.001 TYR R 857 ARG 0.007 0.000 ARG I 902 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 551 time to evaluate : 5.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 896 MET cc_start: 0.7757 (mtm) cc_final: 0.7374 (mtm) REVERT: I 970 ASN cc_start: 0.8646 (m-40) cc_final: 0.8326 (m-40) REVERT: I 1221 MET cc_start: 0.7997 (tpp) cc_final: 0.7698 (tpp) REVERT: K 301 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7834 (mtpt) REVERT: K 430 LEU cc_start: 0.8559 (mt) cc_final: 0.8275 (mt) REVERT: K 441 MET cc_start: 0.8824 (mpp) cc_final: 0.8570 (mpp) REVERT: K 621 ASN cc_start: 0.8618 (m110) cc_final: 0.8409 (t0) REVERT: L 308 GLN cc_start: 0.9050 (tp40) cc_final: 0.8839 (tp40) REVERT: M 35 LEU cc_start: 0.8822 (mm) cc_final: 0.8217 (mt) REVERT: R 285 ASN cc_start: 0.9106 (t0) cc_final: 0.8688 (t0) REVERT: R 569 ARG cc_start: 0.2996 (mmt180) cc_final: -0.0089 (mmt180) REVERT: R 607 MET cc_start: 0.7177 (mmt) cc_final: 0.6585 (mmm) REVERT: R 770 MET cc_start: 0.6614 (ttt) cc_final: 0.6173 (ttm) REVERT: R 853 MET cc_start: 0.8001 (ppp) cc_final: 0.7749 (ppp) REVERT: R 1291 MET cc_start: 0.7733 (ppp) cc_final: 0.7454 (ppp) REVERT: S 101 MET cc_start: 0.8744 (tmm) cc_final: 0.8439 (tmm) REVERT: S 166 GLU cc_start: 0.8806 (tp30) cc_final: 0.8221 (tp30) REVERT: T 36 ARG cc_start: 0.9189 (ttt180) cc_final: 0.8536 (mmm160) REVERT: T 45 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7401 (mm-30) REVERT: T 98 LEU cc_start: 0.8863 (tp) cc_final: 0.8656 (tt) REVERT: T 116 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8164 (tp30) REVERT: T 195 PHE cc_start: 0.8328 (m-80) cc_final: 0.8100 (m-80) REVERT: X 106 GLU cc_start: 0.8963 (tp30) cc_final: 0.8526 (tp30) REVERT: Y 91 LYS cc_start: 0.9286 (tttp) cc_final: 0.9052 (ttpt) outliers start: 1 outliers final: 0 residues processed: 552 average time/residue: 0.5436 time to fit residues: 517.3114 Evaluate side-chains 420 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 369 optimal weight: 0.0770 chunk 206 optimal weight: 8.9990 chunk 553 optimal weight: 0.9980 chunk 452 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 665 optimal weight: 1.9990 chunk 719 optimal weight: 6.9990 chunk 593 optimal weight: 30.0000 chunk 660 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 534 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 270 HIS ** K 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS L 371 HIS L 526 GLN R 219 ASN R 333 HIS R 618 HIS R 802 HIS ** R1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 370 GLN S 470 ASN S 728 HIS ** W 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 48093 Z= 0.177 Angle : 0.610 11.269 66137 Z= 0.309 Chirality : 0.040 0.258 8155 Planarity : 0.004 0.067 8766 Dihedral : 4.771 51.884 7613 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.44 % Favored : 86.44 % Rotamer: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.60 % Twisted General : 0.12 % 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: -1.72 (0.11), residues: 6682 helix: 1.44 (0.09), residues: 3318 sheet: -3.19 (0.24), residues: 401 loop : -4.16 (0.10), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP T 97 HIS 0.014 0.001 HIS S 728 PHE 0.034 0.001 PHE S 340 TYR 0.023 0.001 TYR K 230 ARG 0.013 0.000 ARG R 864 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 528 time to evaluate : 5.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 970 ASN cc_start: 0.8683 (m-40) cc_final: 0.8316 (m-40) REVERT: I 1221 MET cc_start: 0.7883 (tpp) cc_final: 0.7535 (tpp) REVERT: K 430 LEU cc_start: 0.8582 (mt) cc_final: 0.8290 (mt) REVERT: K 441 MET cc_start: 0.8858 (mpp) cc_final: 0.8606 (mpp) REVERT: K 469 MET cc_start: 0.8034 (tpp) cc_final: 0.7767 (tpp) REVERT: K 621 ASN cc_start: 0.8587 (m110) cc_final: 0.8381 (t0) REVERT: M 35 LEU cc_start: 0.8831 (mm) cc_final: 0.8325 (mt) REVERT: M 135 LEU cc_start: 0.8353 (tp) cc_final: 0.7818 (pp) REVERT: R 85 MET cc_start: 0.8707 (tmm) cc_final: 0.8468 (tmm) REVERT: R 569 ARG cc_start: 0.2800 (mmt180) cc_final: -0.0116 (mmt180) REVERT: R 832 TYR cc_start: 0.8373 (m-80) cc_final: 0.7997 (m-80) REVERT: R 1277 MET cc_start: 0.9060 (tpp) cc_final: 0.8796 (tpt) REVERT: R 1291 MET cc_start: 0.7646 (ppp) cc_final: 0.7243 (ppp) REVERT: S 72 MET cc_start: 0.7819 (pmm) cc_final: 0.7565 (pmm) REVERT: S 101 MET cc_start: 0.8874 (tmm) cc_final: 0.8535 (tmm) REVERT: S 166 GLU cc_start: 0.8812 (tp30) cc_final: 0.8201 (tp30) REVERT: S 183 LEU cc_start: 0.8938 (mm) cc_final: 0.8702 (mm) REVERT: S 695 TYR cc_start: 0.7383 (m-80) cc_final: 0.6930 (m-80) REVERT: T 36 ARG cc_start: 0.9201 (ttt180) cc_final: 0.8549 (mmp-170) REVERT: T 45 GLU cc_start: 0.8717 (mt-10) cc_final: 0.7436 (mm-30) REVERT: T 97 TRP cc_start: 0.7465 (p90) cc_final: 0.7228 (p90) REVERT: Y 91 LYS cc_start: 0.9265 (tttp) cc_final: 0.9045 (ttpt) outliers start: 1 outliers final: 0 residues processed: 529 average time/residue: 0.5507 time to fit residues: 504.1637 Evaluate side-chains 424 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 5.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 657 optimal weight: 7.9990 chunk 500 optimal weight: 0.7980 chunk 345 optimal weight: 0.2980 chunk 73 optimal weight: 80.0000 chunk 317 optimal weight: 50.0000 chunk 447 optimal weight: 1.9990 chunk 668 optimal weight: 6.9990 chunk 707 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 633 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN ** K 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN R 552 HIS ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 802 HIS ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN T 209 GLN ** W 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 48093 Z= 0.217 Angle : 0.635 11.366 66137 Z= 0.323 Chirality : 0.041 0.189 8155 Planarity : 0.004 0.068 8766 Dihedral : 4.864 50.569 7613 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.34 % Favored : 85.54 % Rotamer: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.91 % Twisted General : 0.12 % 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: -1.49 (0.11), residues: 6682 helix: 1.65 (0.10), residues: 3309 sheet: -3.05 (0.24), residues: 408 loop : -4.07 (0.10), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 327 HIS 0.012 0.001 HIS R 552 PHE 0.033 0.002 PHE S 340 TYR 0.026 0.002 TYR K 230 ARG 0.007 0.000 ARG R 864 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 516 time to evaluate : 5.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 705 LYS cc_start: 0.9422 (mmmm) cc_final: 0.8794 (mmmm) REVERT: I 708 ASP cc_start: 0.8532 (t70) cc_final: 0.8053 (p0) REVERT: I 970 ASN cc_start: 0.8692 (m-40) cc_final: 0.8269 (m110) REVERT: I 1221 MET cc_start: 0.8031 (tpp) cc_final: 0.7634 (tpp) REVERT: K 92 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.6072 (mm110) REVERT: K 430 LEU cc_start: 0.8715 (mt) cc_final: 0.8424 (mt) REVERT: K 469 MET cc_start: 0.8010 (tpp) cc_final: 0.7674 (tpp) REVERT: K 621 ASN cc_start: 0.8611 (m110) cc_final: 0.8409 (t0) REVERT: L 381 HIS cc_start: 0.8229 (t-90) cc_final: 0.7954 (t-90) REVERT: M 35 LEU cc_start: 0.8840 (mm) cc_final: 0.8226 (mt) REVERT: Q 106 ARG cc_start: 0.8465 (mpt-90) cc_final: 0.8247 (mpt-90) REVERT: R 85 MET cc_start: 0.8672 (tmm) cc_final: 0.8409 (tmm) REVERT: R 333 HIS cc_start: 0.7788 (m-70) cc_final: 0.7417 (m-70) REVERT: R 796 MET cc_start: 0.7666 (mpp) cc_final: 0.7272 (mpp) REVERT: R 922 MET cc_start: 0.8192 (mtm) cc_final: 0.7934 (mtp) REVERT: R 1291 MET cc_start: 0.7829 (ppp) cc_final: 0.7456 (ppp) REVERT: S 101 MET cc_start: 0.8959 (tmm) cc_final: 0.8590 (tmm) REVERT: S 166 GLU cc_start: 0.8799 (tp30) cc_final: 0.8239 (tp30) REVERT: S 183 LEU cc_start: 0.8998 (mm) cc_final: 0.8737 (mm) REVERT: S 709 LEU cc_start: 0.8458 (tt) cc_final: 0.8254 (tt) REVERT: T 36 ARG cc_start: 0.9213 (ttt180) cc_final: 0.8546 (mmp-170) REVERT: T 45 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7453 (mm-30) REVERT: X 106 GLU cc_start: 0.8988 (tp30) cc_final: 0.8695 (tp30) REVERT: Y 91 LYS cc_start: 0.9268 (tttp) cc_final: 0.9053 (ttpt) outliers start: 2 outliers final: 1 residues processed: 518 average time/residue: 0.5276 time to fit residues: 474.5935 Evaluate side-chains 419 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 417 time to evaluate : 5.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 589 optimal weight: 9.9990 chunk 401 optimal weight: 50.0000 chunk 10 optimal weight: 30.0000 chunk 526 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 603 optimal weight: 0.9980 chunk 489 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 361 optimal weight: 0.9990 chunk 635 optimal weight: 0.0970 chunk 178 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 317 GLN I 553 GLN I 859 HIS ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS ** K 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 745 GLN R 802 HIS R 842 GLN ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1197 HIS S 697 ASN ** W 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 97 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 48093 Z= 0.241 Angle : 0.654 12.268 66137 Z= 0.333 Chirality : 0.041 0.316 8155 Planarity : 0.004 0.070 8766 Dihedral : 5.007 48.456 7613 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.94 % Favored : 84.93 % Rotamer: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.91 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 6682 helix: 1.76 (0.10), residues: 3307 sheet: -2.85 (0.25), residues: 387 loop : -4.09 (0.10), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP T 97 HIS 0.007 0.001 HIS J 782 PHE 0.025 0.002 PHE K 677 TYR 0.020 0.002 TYR X 59 ARG 0.006 0.000 ARG R 962 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 502 time to evaluate : 5.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1221 MET cc_start: 0.8007 (tpp) cc_final: 0.7629 (tpp) REVERT: K 621 ASN cc_start: 0.8631 (m110) cc_final: 0.8422 (t0) REVERT: L 381 HIS cc_start: 0.8162 (t-90) cc_final: 0.7911 (t-90) REVERT: L 474 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8549 (ttmm) REVERT: M 35 LEU cc_start: 0.8832 (mm) cc_final: 0.8308 (mt) REVERT: Q 106 ARG cc_start: 0.8588 (mpt-90) cc_final: 0.8251 (mpt-90) REVERT: R 85 MET cc_start: 0.8667 (tmm) cc_final: 0.8370 (tmm) REVERT: R 619 TYR cc_start: 0.9121 (m-80) cc_final: 0.8596 (m-10) REVERT: R 796 MET cc_start: 0.7600 (mpp) cc_final: 0.7279 (mpp) REVERT: R 832 TYR cc_start: 0.8493 (m-80) cc_final: 0.7942 (m-80) REVERT: R 922 MET cc_start: 0.8269 (mtm) cc_final: 0.8023 (mtp) REVERT: R 963 PHE cc_start: 0.8146 (t80) cc_final: 0.7829 (t80) REVERT: R 995 TYR cc_start: 0.8292 (m-80) cc_final: 0.7955 (m-80) REVERT: R 1291 MET cc_start: 0.7570 (ppp) cc_final: 0.7096 (ppp) REVERT: S 72 MET cc_start: 0.7920 (pmm) cc_final: 0.7705 (pmm) REVERT: S 101 MET cc_start: 0.9014 (tmm) cc_final: 0.8593 (tmm) REVERT: S 166 GLU cc_start: 0.8771 (tp30) cc_final: 0.8216 (tp30) REVERT: S 183 LEU cc_start: 0.9025 (mm) cc_final: 0.8734 (mm) REVERT: S 709 LEU cc_start: 0.8519 (tt) cc_final: 0.8305 (tt) REVERT: T 36 ARG cc_start: 0.9231 (ttt180) cc_final: 0.8546 (mmp-170) REVERT: T 45 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7478 (mm-30) REVERT: Y 91 LYS cc_start: 0.9283 (tttp) cc_final: 0.9042 (ttpt) outliers start: 1 outliers final: 0 residues processed: 503 average time/residue: 0.5487 time to fit residues: 481.6182 Evaluate side-chains 409 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 238 optimal weight: 8.9990 chunk 637 optimal weight: 0.2980 chunk 139 optimal weight: 0.0470 chunk 415 optimal weight: 50.0000 chunk 174 optimal weight: 5.9990 chunk 708 optimal weight: 10.0000 chunk 587 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 58 optimal weight: 50.0000 chunk 234 optimal weight: 4.9990 chunk 371 optimal weight: 40.0000 overall best weight: 2.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 637 HIS J 693 ASN ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 333 HIS ** R 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN S 728 HIS ** T 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48093 Z= 0.221 Angle : 0.646 13.051 66137 Z= 0.328 Chirality : 0.041 0.235 8155 Planarity : 0.004 0.070 8766 Dihedral : 5.013 54.876 7613 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.68 % Favored : 85.18 % Rotamer: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.91 % Twisted General : 0.14 % 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: -1.32 (0.11), residues: 6682 helix: 1.81 (0.10), residues: 3302 sheet: -2.85 (0.25), residues: 392 loop : -4.01 (0.10), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP S 23 HIS 0.010 0.001 HIS R 56 PHE 0.038 0.002 PHE S 340 TYR 0.022 0.002 TYR I 335 ARG 0.010 0.000 ARG T 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 5.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 680 GLU cc_start: 0.6449 (pt0) cc_final: 0.6154 (pt0) REVERT: I 1221 MET cc_start: 0.7999 (tpp) cc_final: 0.7606 (tpp) REVERT: K 441 MET cc_start: 0.8934 (mpp) cc_final: 0.8710 (mpp) REVERT: K 469 MET cc_start: 0.8189 (tpp) cc_final: 0.7886 (tpp) REVERT: K 492 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8022 (mp0) REVERT: K 644 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: L 381 HIS cc_start: 0.8135 (t-90) cc_final: 0.7847 (t-90) REVERT: M 35 LEU cc_start: 0.8866 (mm) cc_final: 0.8295 (mt) REVERT: R 85 MET cc_start: 0.8652 (tmm) cc_final: 0.8375 (tmm) REVERT: R 619 TYR cc_start: 0.9177 (m-80) cc_final: 0.8641 (m-10) REVERT: R 796 MET cc_start: 0.7617 (mpp) cc_final: 0.7331 (mpp) REVERT: R 832 TYR cc_start: 0.8552 (m-80) cc_final: 0.8005 (m-80) REVERT: R 963 PHE cc_start: 0.8185 (t80) cc_final: 0.7846 (t80) REVERT: R 1089 ASN cc_start: 0.6653 (m-40) cc_final: 0.6066 (t0) REVERT: R 1277 MET cc_start: 0.8988 (tpp) cc_final: 0.8618 (tpt) REVERT: R 1291 MET cc_start: 0.7633 (ppp) cc_final: 0.7101 (ppp) REVERT: S 101 MET cc_start: 0.9021 (tmm) cc_final: 0.8669 (tmm) REVERT: S 166 GLU cc_start: 0.8773 (tp30) cc_final: 0.8205 (tp30) REVERT: T 36 ARG cc_start: 0.9240 (ttt180) cc_final: 0.8550 (mmp-170) REVERT: T 45 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7398 (mm-30) REVERT: Y 91 LYS cc_start: 0.9275 (tttp) cc_final: 0.9022 (ttpt) outliers start: 1 outliers final: 0 residues processed: 504 average time/residue: 0.5331 time to fit residues: 467.0114 Evaluate side-chains 410 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 5.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 682 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 403 optimal weight: 80.0000 chunk 517 optimal weight: 1.9990 chunk 400 optimal weight: 7.9990 chunk 596 optimal weight: 5.9990 chunk 395 optimal weight: 0.0970 chunk 705 optimal weight: 1.9990 chunk 441 optimal weight: 0.8980 chunk 430 optimal weight: 3.9990 chunk 325 optimal weight: 0.0770 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 693 ASN ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 GLN R 333 HIS ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN ** W 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 48093 Z= 0.170 Angle : 0.621 14.521 66137 Z= 0.312 Chirality : 0.040 0.196 8155 Planarity : 0.004 0.069 8766 Dihedral : 4.856 50.689 7613 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.66 % Favored : 86.25 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.60 % Twisted General : 0.12 % 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: -1.18 (0.11), residues: 6682 helix: 1.94 (0.10), residues: 3300 sheet: -2.77 (0.25), residues: 395 loop : -3.96 (0.10), residues: 2987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP S 23 HIS 0.008 0.001 HIS R 56 PHE 0.034 0.001 PHE S 340 TYR 0.032 0.001 TYR R1249 ARG 0.006 0.000 ARG R 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 5.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 708 ASP cc_start: 0.8533 (t70) cc_final: 0.7953 (p0) REVERT: I 970 ASN cc_start: 0.8712 (m-40) cc_final: 0.8309 (m110) REVERT: I 1221 MET cc_start: 0.7903 (tpp) cc_final: 0.7479 (tpp) REVERT: K 469 MET cc_start: 0.8155 (tpp) cc_final: 0.7868 (tpp) REVERT: K 492 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8139 (mp0) REVERT: L 381 HIS cc_start: 0.8092 (t-90) cc_final: 0.7802 (t-90) REVERT: M 35 LEU cc_start: 0.8781 (mm) cc_final: 0.8339 (mt) REVERT: Q 106 ARG cc_start: 0.8639 (mpt-90) cc_final: 0.8279 (mpt-90) REVERT: R 85 MET cc_start: 0.8598 (tmm) cc_final: 0.8327 (tmm) REVERT: R 569 ARG cc_start: 0.3244 (mmt180) cc_final: 0.1172 (mmt180) REVERT: R 619 TYR cc_start: 0.9163 (m-80) cc_final: 0.8640 (m-10) REVERT: R 796 MET cc_start: 0.7558 (mpp) cc_final: 0.7218 (mpp) REVERT: R 832 TYR cc_start: 0.8447 (m-80) cc_final: 0.7949 (m-80) REVERT: R 853 MET cc_start: 0.8015 (ppp) cc_final: 0.7570 (ppp) REVERT: R 859 ILE cc_start: 0.7919 (tp) cc_final: 0.7618 (mm) REVERT: R 963 PHE cc_start: 0.8116 (t80) cc_final: 0.7768 (t80) REVERT: R 1277 MET cc_start: 0.8995 (tpp) cc_final: 0.8581 (tpt) REVERT: R 1291 MET cc_start: 0.7656 (ppp) cc_final: 0.7058 (ppp) REVERT: S 72 MET cc_start: 0.7926 (pmm) cc_final: 0.7654 (pmm) REVERT: S 101 MET cc_start: 0.9036 (tmm) cc_final: 0.8631 (tmm) REVERT: S 166 GLU cc_start: 0.8768 (tp30) cc_final: 0.8176 (tp30) REVERT: T 36 ARG cc_start: 0.9222 (ttt180) cc_final: 0.8550 (mmp-170) REVERT: T 45 GLU cc_start: 0.8645 (mt-10) cc_final: 0.7362 (mm-30) REVERT: T 92 TYR cc_start: 0.8458 (t80) cc_final: 0.8101 (t80) REVERT: T 94 PHE cc_start: 0.8224 (t80) cc_final: 0.7932 (t80) REVERT: X 106 GLU cc_start: 0.8919 (tp30) cc_final: 0.8624 (tp30) REVERT: Y 91 LYS cc_start: 0.9263 (tttp) cc_final: 0.8995 (ttpt) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.5281 time to fit residues: 474.8933 Evaluate side-chains 422 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 5.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 436 optimal weight: 0.8980 chunk 281 optimal weight: 8.9990 chunk 421 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 136 optimal weight: 0.4980 chunk 448 optimal weight: 3.9990 chunk 480 optimal weight: 3.9990 chunk 348 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 554 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 333 HIS ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 708 GLN ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN ** W 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 48093 Z= 0.179 Angle : 0.628 14.824 66137 Z= 0.314 Chirality : 0.041 0.406 8155 Planarity : 0.004 0.074 8766 Dihedral : 4.803 48.822 7613 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.14 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.60 % Twisted General : 0.12 % 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: -1.09 (0.11), residues: 6682 helix: 2.01 (0.10), residues: 3308 sheet: -2.70 (0.25), residues: 397 loop : -3.93 (0.10), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP S 23 HIS 0.010 0.001 HIS R 918 PHE 0.029 0.001 PHE S 340 TYR 0.024 0.001 TYR R1249 ARG 0.008 0.000 ARG J 631 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 5.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 680 GLU cc_start: 0.6249 (pt0) cc_final: 0.5957 (pt0) REVERT: I 708 ASP cc_start: 0.8564 (t70) cc_final: 0.7953 (p0) REVERT: I 970 ASN cc_start: 0.8675 (m-40) cc_final: 0.8431 (m-40) REVERT: I 971 MET cc_start: 0.8532 (mmm) cc_final: 0.8332 (tpp) REVERT: I 1221 MET cc_start: 0.7926 (tpp) cc_final: 0.7501 (tpp) REVERT: K 469 MET cc_start: 0.8137 (tpp) cc_final: 0.7874 (tpp) REVERT: K 492 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8133 (mp0) REVERT: L 381 HIS cc_start: 0.8165 (t-90) cc_final: 0.7868 (t-90) REVERT: M 35 LEU cc_start: 0.8802 (mm) cc_final: 0.8455 (mt) REVERT: M 135 LEU cc_start: 0.8367 (tp) cc_final: 0.7814 (pp) REVERT: Q 106 ARG cc_start: 0.8705 (mpt-90) cc_final: 0.8387 (mtt90) REVERT: R 85 MET cc_start: 0.8598 (tmm) cc_final: 0.8318 (tmm) REVERT: R 569 ARG cc_start: 0.3481 (mmt180) cc_final: 0.1314 (mmt180) REVERT: R 619 TYR cc_start: 0.9156 (m-80) cc_final: 0.8634 (m-10) REVERT: R 832 TYR cc_start: 0.8467 (m-80) cc_final: 0.7942 (m-80) REVERT: R 859 ILE cc_start: 0.7945 (tp) cc_final: 0.7661 (mm) REVERT: R 963 PHE cc_start: 0.8114 (t80) cc_final: 0.7591 (t80) REVERT: R 1038 ARG cc_start: 0.6335 (ptp-110) cc_final: 0.6013 (mmt180) REVERT: R 1291 MET cc_start: 0.7719 (ppp) cc_final: 0.7113 (ppp) REVERT: S 101 MET cc_start: 0.9074 (tmm) cc_final: 0.8575 (tmm) REVERT: S 166 GLU cc_start: 0.8758 (tp30) cc_final: 0.8212 (tp30) REVERT: T 36 ARG cc_start: 0.9227 (ttt180) cc_final: 0.8560 (mmp-170) REVERT: T 45 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7808 (mm-30) REVERT: Y 91 LYS cc_start: 0.9268 (tttp) cc_final: 0.9002 (ttpt) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.5519 time to fit residues: 476.8793 Evaluate side-chains 415 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 4.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 641 optimal weight: 4.9990 chunk 675 optimal weight: 2.9990 chunk 616 optimal weight: 0.9980 chunk 657 optimal weight: 3.9990 chunk 395 optimal weight: 0.0470 chunk 286 optimal weight: 0.9980 chunk 516 optimal weight: 4.9990 chunk 201 optimal weight: 0.2980 chunk 594 optimal weight: 0.9990 chunk 621 optimal weight: 0.7980 chunk 655 optimal weight: 0.0970 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 416 HIS ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 ASN R 333 HIS ** R 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 907 ASN ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 48093 Z= 0.160 Angle : 0.622 15.796 66137 Z= 0.309 Chirality : 0.040 0.322 8155 Planarity : 0.004 0.072 8766 Dihedral : 4.670 54.246 7613 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.96 % Favored : 86.96 % Rotamer: Outliers : 0.03 % Allowed : 0.92 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.60 % Twisted General : 0.12 % 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: -1.01 (0.11), residues: 6682 helix: 2.08 (0.10), residues: 3308 sheet: -2.72 (0.24), residues: 414 loop : -3.90 (0.10), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP T 97 HIS 0.010 0.001 HIS I 686 PHE 0.022 0.001 PHE V 208 TYR 0.019 0.001 TYR X 59 ARG 0.008 0.000 ARG I 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 515 time to evaluate : 5.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 680 GLU cc_start: 0.6204 (pt0) cc_final: 0.5923 (pt0) REVERT: I 708 ASP cc_start: 0.8491 (t70) cc_final: 0.7933 (p0) REVERT: I 970 ASN cc_start: 0.8592 (m-40) cc_final: 0.8357 (m-40) REVERT: I 1220 ILE cc_start: 0.8872 (pt) cc_final: 0.8610 (tt) REVERT: I 1221 MET cc_start: 0.7915 (tpp) cc_final: 0.7610 (mmt) REVERT: J 647 MET cc_start: 0.8511 (mmp) cc_final: 0.8283 (mmp) REVERT: K 444 ILE cc_start: 0.7713 (tp) cc_final: 0.7397 (mt) REVERT: K 469 MET cc_start: 0.8079 (tpp) cc_final: 0.7832 (tpp) REVERT: L 381 HIS cc_start: 0.8109 (t-90) cc_final: 0.7830 (t-90) REVERT: M 35 LEU cc_start: 0.8775 (mm) cc_final: 0.8335 (mt) REVERT: M 135 LEU cc_start: 0.8367 (tp) cc_final: 0.7846 (pp) REVERT: Q 106 ARG cc_start: 0.8709 (mpt-90) cc_final: 0.8347 (mpt-90) REVERT: R 85 MET cc_start: 0.8491 (tmm) cc_final: 0.8218 (tmm) REVERT: R 619 TYR cc_start: 0.9159 (m-80) cc_final: 0.8652 (m-10) REVERT: R 832 TYR cc_start: 0.8479 (m-80) cc_final: 0.7951 (m-80) REVERT: R 853 MET cc_start: 0.8023 (ppp) cc_final: 0.7552 (ppp) REVERT: R 859 ILE cc_start: 0.7949 (tp) cc_final: 0.7707 (mm) REVERT: R 963 PHE cc_start: 0.8135 (t80) cc_final: 0.7670 (t80) REVERT: R 1012 TYR cc_start: 0.1379 (m-80) cc_final: 0.1011 (m-80) REVERT: R 1291 MET cc_start: 0.7578 (ppp) cc_final: 0.7004 (ppp) REVERT: S 72 MET cc_start: 0.7853 (pmm) cc_final: 0.7631 (pmm) REVERT: S 166 GLU cc_start: 0.8752 (tp30) cc_final: 0.8187 (tp30) REVERT: T 36 ARG cc_start: 0.9237 (ttt180) cc_final: 0.8563 (mmp-170) REVERT: T 45 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7425 (mm-30) REVERT: X 106 GLU cc_start: 0.8929 (tp30) cc_final: 0.8589 (tp30) REVERT: Y 91 LYS cc_start: 0.9255 (tttp) cc_final: 0.8982 (ttpt) outliers start: 1 outliers final: 0 residues processed: 516 average time/residue: 0.5732 time to fit residues: 519.5092 Evaluate side-chains 424 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 431 optimal weight: 4.9990 chunk 695 optimal weight: 0.9990 chunk 424 optimal weight: 7.9990 chunk 329 optimal weight: 5.9990 chunk 483 optimal weight: 0.9980 chunk 729 optimal weight: 50.0000 chunk 671 optimal weight: 0.6980 chunk 580 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 448 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 686 HIS J 637 HIS ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS R 333 HIS ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 245 HIS S 697 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 48093 Z= 0.194 Angle : 0.641 15.051 66137 Z= 0.321 Chirality : 0.041 0.294 8155 Planarity : 0.004 0.070 8766 Dihedral : 4.710 52.611 7613 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.14 % Favored : 85.77 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.60 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 6682 helix: 2.08 (0.10), residues: 3315 sheet: -2.73 (0.24), residues: 419 loop : -3.87 (0.10), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP T 97 HIS 0.011 0.001 HIS J 768 PHE 0.049 0.002 PHE S 340 TYR 0.019 0.001 TYR X 59 ARG 0.009 0.000 ARG I 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13364 Ramachandran restraints generated. 6682 Oldfield, 0 Emsley, 6682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 5.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 708 ASP cc_start: 0.8583 (t70) cc_final: 0.7963 (p0) REVERT: I 970 ASN cc_start: 0.8686 (m-40) cc_final: 0.8306 (m-40) REVERT: I 1221 MET cc_start: 0.7950 (tpp) cc_final: 0.7528 (tpp) REVERT: K 441 MET cc_start: 0.8646 (mpp) cc_final: 0.8380 (mpp) REVERT: K 444 ILE cc_start: 0.7748 (tp) cc_final: 0.7491 (mt) REVERT: K 469 MET cc_start: 0.8118 (tpp) cc_final: 0.7849 (tpp) REVERT: K 492 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7998 (mp0) REVERT: L 381 HIS cc_start: 0.8189 (t-90) cc_final: 0.7942 (t-90) REVERT: M 32 LEU cc_start: 0.8987 (tt) cc_final: 0.8714 (tt) REVERT: M 35 LEU cc_start: 0.8818 (mm) cc_final: 0.8458 (pp) REVERT: M 135 LEU cc_start: 0.8390 (tp) cc_final: 0.7866 (pp) REVERT: Q 106 ARG cc_start: 0.8777 (mpt-90) cc_final: 0.8401 (mpt-90) REVERT: R 85 MET cc_start: 0.8620 (tmm) cc_final: 0.8304 (tmm) REVERT: R 619 TYR cc_start: 0.9191 (m-80) cc_final: 0.8689 (m-10) REVERT: R 832 TYR cc_start: 0.8496 (m-80) cc_final: 0.7954 (m-80) REVERT: R 853 MET cc_start: 0.8081 (ppp) cc_final: 0.7620 (ppp) REVERT: R 859 ILE cc_start: 0.7978 (tp) cc_final: 0.7735 (mm) REVERT: R 963 PHE cc_start: 0.8146 (t80) cc_final: 0.7617 (t80) REVERT: R 1291 MET cc_start: 0.7653 (ppp) cc_final: 0.7007 (ppp) REVERT: S 166 GLU cc_start: 0.8759 (tp30) cc_final: 0.8220 (tp30) REVERT: T 36 ARG cc_start: 0.9247 (ttt180) cc_final: 0.8563 (mmp-170) REVERT: T 45 GLU cc_start: 0.8700 (mt-10) cc_final: 0.7854 (mm-30) REVERT: T 92 TYR cc_start: 0.8401 (t80) cc_final: 0.8111 (t80) REVERT: Y 91 LYS cc_start: 0.9261 (tttp) cc_final: 0.8994 (ttpt) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.5345 time to fit residues: 464.4273 Evaluate side-chains 405 residues out of total 6132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 5.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 732 random chunks: chunk 461 optimal weight: 10.0000 chunk 618 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 535 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 581 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 597 optimal weight: 9.9990 chunk 73 optimal weight: 80.0000 chunk 107 optimal weight: 50.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 686 HIS ** J 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS R 333 HIS ** R 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.083462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.067194 restraints weight = 324650.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.068300 restraints weight = 198870.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.068881 restraints weight = 139967.109| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 48093 Z= 0.201 Angle : 0.640 14.996 66137 Z= 0.321 Chirality : 0.041 0.304 8155 Planarity : 0.004 0.069 8766 Dihedral : 4.792 53.640 7613 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.29 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.30 % Cis-general : 0.12 % Twisted Proline : 0.91 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.11), residues: 6682 helix: 2.08 (0.10), residues: 3325 sheet: -2.69 (0.25), residues: 404 loop : -3.88 (0.10), residues: 2953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP T 97 HIS 0.011 0.001 HIS R 802 PHE 0.035 0.002 PHE S 340 TYR 0.053 0.001 TYR R1249 ARG 0.009 0.000 ARG I 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10475.96 seconds wall clock time: 188 minutes 13.49 seconds (11293.49 seconds total)