Starting phenix.real_space_refine on Fri Mar 22 20:07:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/03_2024/7ast_11904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/03_2024/7ast_11904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/03_2024/7ast_11904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/03_2024/7ast_11904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/03_2024/7ast_11904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/03_2024/7ast_11904.pdb" } resolution = 4.0 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= 0.001 sd= 0.006 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 236 5.16 5 C 21859 2.51 5 N 6002 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N ASP 45": "OD1" <-> "OD2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 148": "OD1" <-> "OD2" Residue "N PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 213": "NH1" <-> "NH2" Residue "N PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 376": "NH1" <-> "NH2" Residue "N PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 582": "NH1" <-> "NH2" Residue "N ASP 651": "OD1" <-> "OD2" Residue "N TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 678": "OD1" <-> "OD2" Residue "N TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 745": "OE1" <-> "OE2" Residue "N ARG 760": "NH1" <-> "NH2" Residue "N ASP 772": "OD1" <-> "OD2" Residue "N ARG 816": "NH1" <-> "NH2" Residue "N GLU 867": "OE1" <-> "OE2" Residue "N TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 1005": "NH1" <-> "NH2" Residue "N GLU 1147": "OE1" <-> "OE2" Residue "N TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 1306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 1338": "OD1" <-> "OD2" Residue "N GLU 1345": "OE1" <-> "OE2" Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 69": "OD1" <-> "OD2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 145": "NH1" <-> "NH2" Residue "H ARG 191": "NH1" <-> "NH2" Residue "H ARG 274": "NH1" <-> "NH2" Residue "H ASP 281": "OD1" <-> "OD2" Residue "H PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 303": "NH1" <-> "NH2" Residue "H TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 335": "NH1" <-> "NH2" Residue "H PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "J PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 24": "OD1" <-> "OD2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J ASP 143": "OD1" <-> "OD2" Residue "J PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 188": "NH1" <-> "NH2" Residue "M TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 307": "OE1" <-> "OE2" Residue "M PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 329": "NH1" <-> "NH2" Residue "M ASP 352": "OD1" <-> "OD2" Residue "M TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 522": "OD1" <-> "OD2" Residue "M ARG 563": "NH1" <-> "NH2" Residue "M ASP 580": "OD1" <-> "OD2" Residue "M TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 704": "NH1" <-> "NH2" Residue "M TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 731": "OE1" <-> "OE2" Residue "M TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 763": "OD1" <-> "OD2" Residue "M TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 807": "OE1" <-> "OE2" Residue "M TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 877": "OD1" <-> "OD2" Residue "M ARG 890": "NH1" <-> "NH2" Residue "M GLU 914": "OE1" <-> "OE2" Residue "M ASP 915": "OD1" <-> "OD2" Residue "M ARG 957": "NH1" <-> "NH2" Residue "M TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 1078": "OD1" <-> "OD2" Residue "M TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 1133": "OE1" <-> "OE2" Residue "Z ARG 271": "NH1" <-> "NH2" Residue "X TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 480": "OE1" <-> "OE2" Residue "X GLU 486": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34518 Number of models: 1 Model: "" Number of chains: 17 Chain: "N" Number of atoms: 9385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 9385 Classifications: {'peptide': 1238} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'CIS': 26, 'PCIS': 3, 'PTRANS': 49, 'TRANS': 1159} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 155 Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 288 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "B" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "C" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 972 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 117} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "F" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2635 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 17, 'TRANS': 311} Chain: "I" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1008 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1442 Classifications: {'peptide': 179} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 168} Chain breaks: 1 Chain: "K" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "M" Number of atoms: 8811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8811 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1061} Chain: "Z" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 2 Chain: "X" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 9, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 17.74, per 1000 atoms: 0.51 Number of scatterers: 34518 At special positions: 0 Unit cell: (187.44, 146.97, 164.01, 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 236 16.00 O 6421 8.00 N 6002 7.00 C 21859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 69 " - pdb=" SG CYS N 79 " distance=2.03 Simple disulfide: pdb=" SG CYS N 92 " - pdb=" SG CYS N 317 " distance=2.03 Simple disulfide: pdb=" SG CYS N 109 " - pdb=" SG CYS N 159 " distance=2.03 Simple disulfide: pdb=" SG CYS N 960 " - pdb=" SG CYS N 961 " distance=2.04 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 25 " distance=2.05 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 28 " distance=2.02 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS M1083 " - pdb=" SG CYS M1095 " 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: 13.14 Conformation dependent library (CDL) restraints added in 5.8 seconds 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8266 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 36 sheets defined 34.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'N' and resid 24 through 31 removed outlier: 4.368A pdb=" N GLN N 31 " --> pdb=" O GLU N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 105 Processing helix chain 'N' and resid 121 through 130 removed outlier: 4.396A pdb=" N PHE N 125 " --> pdb=" O GLU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 147 removed outlier: 4.293A pdb=" N ARG N 140 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS N 145 " --> pdb=" O GLY N 141 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER N 147 " --> pdb=" O LYS N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 228 removed outlier: 3.920A pdb=" N VAL N 223 " --> pdb=" O ASN N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 285 removed outlier: 4.137A pdb=" N LEU N 283 " --> pdb=" O THR N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 291 removed outlier: 3.636A pdb=" N ASP N 291 " --> pdb=" O ILE N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 318 Processing helix chain 'N' and resid 400 through 409 removed outlier: 4.061A pdb=" N LEU N 407 " --> pdb=" O PHE N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 469 through 473 removed outlier: 3.775A pdb=" N ILE N 473 " --> pdb=" O LYS N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 493 removed outlier: 4.111A pdb=" N CYS N 493 " --> pdb=" O GLU N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 515 through 521 Processing helix chain 'N' and resid 544 through 554 Processing helix chain 'N' and resid 565 through 570 removed outlier: 3.696A pdb=" N ALA N 569 " --> pdb=" O GLN N 566 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 602 removed outlier: 3.673A pdb=" N PHE N 601 " --> pdb=" O GLY N 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 651 through 656 Processing helix chain 'N' and resid 679 through 687 Processing helix chain 'N' and resid 690 through 694 Processing helix chain 'N' and resid 710 through 734 removed outlier: 4.339A pdb=" N LEU N 716 " --> pdb=" O ALA N 712 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN N 732 " --> pdb=" O ILE N 728 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR N 733 " --> pdb=" O GLU N 729 " (cutoff:3.500A) Processing helix chain 'N' and resid 744 through 748 removed outlier: 3.622A pdb=" N THR N 747 " --> pdb=" O ALA N 744 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU N 748 " --> pdb=" O GLU N 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 744 through 748' Processing helix chain 'N' and resid 749 through 768 Processing helix chain 'N' and resid 777 through 781 Processing helix chain 'N' and resid 859 through 879 removed outlier: 5.244A pdb=" N THR N 865 " --> pdb=" O THR N 861 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA N 866 " --> pdb=" O ALA N 862 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU N 867 " --> pdb=" O VAL N 863 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY N 869 " --> pdb=" O THR N 865 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR N 870 " --> pdb=" O ALA N 866 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG N 873 " --> pdb=" O GLY N 869 " (cutoff:3.500A) Processing helix chain 'N' and resid 908 through 912 removed outlier: 3.771A pdb=" N ALA N 911 " --> pdb=" O ASP N 908 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET N 912 " --> pdb=" O PRO N 909 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 908 through 912' Processing helix chain 'N' and resid 914 through 915 No H-bonds generated for 'chain 'N' and resid 914 through 915' Processing helix chain 'N' and resid 919 through 921 No H-bonds generated for 'chain 'N' and resid 919 through 921' Processing helix chain 'N' and resid 922 through 930 removed outlier: 3.601A pdb=" N ASP N 926 " --> pdb=" O LYS N 922 " (cutoff:3.500A) Processing helix chain 'N' and resid 942 through 957 Processing helix chain 'N' and resid 967 through 992 removed outlier: 4.108A pdb=" N PHE N 972 " --> pdb=" O GLU N 968 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE N 973 " --> pdb=" O ILE N 969 " (cutoff:3.500A) Processing helix chain 'N' and resid 1001 through 1005 removed outlier: 4.067A pdb=" N ARG N1005 " --> pdb=" O GLN N1002 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1025 Processing helix chain 'N' and resid 1033 through 1043 Processing helix chain 'N' and resid 1044 through 1046 No H-bonds generated for 'chain 'N' and resid 1044 through 1046' Processing helix chain 'N' and resid 1068 through 1076 removed outlier: 3.711A pdb=" N GLU N1072 " --> pdb=" O PRO N1068 " (cutoff:3.500A) Processing helix chain 'N' and resid 1094 through 1106 removed outlier: 4.399A pdb=" N VAL N1101 " --> pdb=" O TYR N1097 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU N1106 " --> pdb=" O LYS N1102 " (cutoff:3.500A) Processing helix chain 'N' and resid 1135 through 1142 removed outlier: 3.847A pdb=" N LEU N1139 " --> pdb=" O GLU N1135 " (cutoff:3.500A) Processing helix chain 'N' and resid 1145 through 1155 Processing helix chain 'N' and resid 1188 through 1194 Processing helix chain 'N' and resid 1242 through 1246 Processing helix chain 'N' and resid 1250 through 1258 removed outlier: 3.643A pdb=" N LYS N1256 " --> pdb=" O TYR N1252 " (cutoff:3.500A) Processing helix chain 'N' and resid 1259 through 1271 Processing helix chain 'N' and resid 1283 through 1295 removed outlier: 3.659A pdb=" N VAL N1287 " --> pdb=" O ASP N1283 " (cutoff:3.500A) Processing helix chain 'N' and resid 1315 through 1320 removed outlier: 3.869A pdb=" N ALA N1319 " --> pdb=" O VAL N1315 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER N1320 " --> pdb=" O LEU N1316 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 1315 through 1320' Processing helix chain 'N' and resid 1325 through 1334 removed outlier: 4.205A pdb=" N PHE N1329 " --> pdb=" O ALA N1325 " (cutoff:3.500A) Processing helix chain 'N' and resid 1343 through 1350 removed outlier: 4.202A pdb=" N ILE N1347 " --> pdb=" O VAL N1343 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE N1348 " --> pdb=" O SER N1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.888A pdb=" N ARG B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 removed outlier: 4.412A pdb=" N LYS B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 76 removed outlier: 4.034A pdb=" N CYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 22 removed outlier: 5.078A pdb=" N TYR F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 36 through 45 Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'F' and resid 111 through 121 Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 178 through 183 removed outlier: 4.060A pdb=" N PHE F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 removed outlier: 3.514A pdb=" N GLY G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 116 removed outlier: 3.581A pdb=" N ALA G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 49 removed outlier: 3.545A pdb=" N PHE H 45 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS H 47 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.593A pdb=" N ALA H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 222 through 226 Processing helix chain 'H' and resid 247 through 250 removed outlier: 3.777A pdb=" N ALA H 250 " --> pdb=" O GLY H 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 247 through 250' Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 286 through 290 removed outlier: 3.971A pdb=" N ASN H 290 " --> pdb=" O ILE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 334 removed outlier: 3.524A pdb=" N MET H 330 " --> pdb=" O ILE H 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 28 removed outlier: 3.527A pdb=" N LYS I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 40 through 56 removed outlier: 3.830A pdb=" N THR I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 Processing helix chain 'I' and resid 73 through 77 removed outlier: 3.786A pdb=" N LYS I 77 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 removed outlier: 3.698A pdb=" N LYS I 83 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 99 removed outlier: 4.155A pdb=" N ILE I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 124 removed outlier: 3.715A pdb=" N LEU I 116 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.733A pdb=" N GLN J 17 " --> pdb=" O PRO J 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 18 " --> pdb=" O PRO J 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 14 through 18' Processing helix chain 'J' and resid 22 through 33 removed outlier: 4.080A pdb=" N LYS J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 70 removed outlier: 4.210A pdb=" N CYS K 70 " --> pdb=" O PRO K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 70' Processing helix chain 'K' and resid 71 through 78 removed outlier: 4.060A pdb=" N ILE K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.774A pdb=" N SER K 112 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 336 removed outlier: 3.887A pdb=" N GLY L 335 " --> pdb=" O ARG L 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 28 removed outlier: 3.520A pdb=" N TRP M 27 " --> pdb=" O VAL M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 41 through 53 Processing helix chain 'M' and resid 53 through 60 Processing helix chain 'M' and resid 235 through 243 Processing helix chain 'M' and resid 247 through 256 removed outlier: 3.601A pdb=" N ILE M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 276 removed outlier: 3.636A pdb=" N MET M 262 " --> pdb=" O GLU M 258 " (cutoff:3.500A) Proline residue: M 267 - end of helix Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 292 through 300 removed outlier: 3.556A pdb=" N MET M 296 " --> pdb=" O ARG M 293 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY M 298 " --> pdb=" O ARG M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 314 Processing helix chain 'M' and resid 315 through 320 Processing helix chain 'M' and resid 328 through 339 Processing helix chain 'M' and resid 364 through 391 Processing helix chain 'M' and resid 410 through 422 Processing helix chain 'M' and resid 445 through 452 removed outlier: 3.658A pdb=" N MET M 452 " --> pdb=" O ALA M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 476 removed outlier: 3.990A pdb=" N GLN M 475 " --> pdb=" O GLN M 472 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP M 476 " --> pdb=" O PRO M 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 472 through 476' Processing helix chain 'M' and resid 508 through 519 removed outlier: 5.103A pdb=" N LEU M 514 " --> pdb=" O PRO M 510 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY M 519 " --> pdb=" O ALA M 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 526 Processing helix chain 'M' and resid 551 through 564 removed outlier: 4.677A pdb=" N ASN M 557 " --> pdb=" O LYS M 553 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 615 Processing helix chain 'M' and resid 635 through 641 Processing helix chain 'M' and resid 660 through 664 removed outlier: 4.073A pdb=" N THR M 663 " --> pdb=" O GLU M 660 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU M 664 " --> pdb=" O PRO M 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 660 through 664' Processing helix chain 'M' and resid 679 through 693 removed outlier: 3.657A pdb=" N ASN M 683 " --> pdb=" O GLN M 679 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS M 691 " --> pdb=" O CYS M 687 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN M 692 " --> pdb=" O ALA M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 700 through 704 Processing helix chain 'M' and resid 722 through 728 removed outlier: 3.516A pdb=" N GLU M 726 " --> pdb=" O THR M 722 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU M 727 " --> pdb=" O LYS M 723 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE M 728 " --> pdb=" O THR M 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 722 through 728' Processing helix chain 'M' and resid 912 through 916 Processing helix chain 'M' and resid 944 through 954 removed outlier: 3.983A pdb=" N LYS M 950 " --> pdb=" O LEU M 946 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 954 " --> pdb=" O LYS M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 968 through 979 removed outlier: 3.976A pdb=" N VAL M 972 " --> pdb=" O LYS M 968 " (cutoff:3.500A) Processing helix chain 'M' and resid 1048 through 1057 Processing helix chain 'M' and resid 1060 through 1070 Processing helix chain 'M' and resid 1107 through 1120 removed outlier: 3.885A pdb=" N LYS M1111 " --> pdb=" O PRO M1107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER M1119 " --> pdb=" O GLN M1115 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET M1120 " --> pdb=" O GLU M1116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 189 removed outlier: 3.565A pdb=" N GLN Z 183 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 222 Processing helix chain 'Z' and resid 231 through 244 removed outlier: 4.431A pdb=" N LEU Z 242 " --> pdb=" O ILE Z 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 17 Processing helix chain 'X' and resid 18 through 32 removed outlier: 3.671A pdb=" N GLU X 22 " --> pdb=" O GLY X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 44 Processing helix chain 'X' and resid 46 through 60 Processing helix chain 'X' and resid 78 through 84 Processing helix chain 'X' and resid 86 through 99 removed outlier: 4.554A pdb=" N ARG X 90 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 112 Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'X' and resid 140 through 154 removed outlier: 3.888A pdb=" N VAL X 144 " --> pdb=" O ASP X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 259 removed outlier: 3.533A pdb=" N PHE X 242 " --> pdb=" O ASN X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 272 removed outlier: 3.525A pdb=" N SER X 264 " --> pdb=" O ASP X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 289 through 296 Processing helix chain 'X' and resid 304 through 317 Processing helix chain 'X' and resid 337 through 357 Processing helix chain 'X' and resid 359 through 370 removed outlier: 3.506A pdb=" N ALA X 363 " --> pdb=" O GLY X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 379 through 385 removed outlier: 4.196A pdb=" N PHE X 383 " --> pdb=" O GLN X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 387 through 402 Processing helix chain 'X' and resid 427 through 456 Processing helix chain 'X' and resid 460 through 477 removed outlier: 3.791A pdb=" N ALA X 476 " --> pdb=" O ALA X 472 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR X 477 " --> pdb=" O SER X 473 " (cutoff:3.500A) Processing helix chain 'X' and resid 480 through 491 removed outlier: 3.921A pdb=" N LEU X 484 " --> pdb=" O GLU X 480 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 530 Processing helix chain 'Y' and resid 3 through 20 removed outlier: 4.224A pdb=" N UNK Y 11 " --> pdb=" O UNK Y 7 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N UNK Y 14 " --> pdb=" O UNK Y 10 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK Y 20 " --> pdb=" O UNK Y 16 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 17 through 18 removed outlier: 4.022A pdb=" N HIS N 17 " --> pdb=" O LYS M1127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 164 through 166 removed outlier: 4.079A pdb=" N THR N 165 " --> pdb=" O HIS N 176 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS N 176 " --> pdb=" O THR N 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'N' and resid 462 through 463 removed outlier: 4.057A pdb=" N ASN N 506 " --> pdb=" O ASN N 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'N' and resid 1215 through 1216 Processing sheet with id=AA6, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.605A pdb=" N ASN A 10 " --> pdb=" O CYS A 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.777A pdb=" N PHE C 55 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 92 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU H 142 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU H 138 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN H 139 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'E' and resid 105 through 108 Processing sheet with id=AB2, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 151 removed outlier: 4.108A pdb=" N VAL F 190 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 40 through 44 removed outlier: 3.667A pdb=" N VAL G 40 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 84 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN G 85 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 66 removed outlier: 4.164A pdb=" N MET H 65 " --> pdb=" O TYR H 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.547A pdb=" N GLU I 2 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET J 7 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE J 72 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'J' and resid 106 through 107 removed outlier: 7.210A pdb=" N ASP J 106 " --> pdb=" O LEU J 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 129 through 131 removed outlier: 3.860A pdb=" N HIS J 138 " --> pdb=" O TYR J 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AC2, first strand: chain 'K' and resid 28 through 29 removed outlier: 3.787A pdb=" N ARG K 136 " --> pdb=" O CYS K 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 208 through 209 Processing sheet with id=AC4, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AC5, first strand: chain 'M' and resid 183 through 184 removed outlier: 3.813A pdb=" N GLN M 183 " --> pdb=" O ARG M 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 191 through 193 removed outlier: 3.723A pdb=" N VAL M 199 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA M 198 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER M 202 " --> pdb=" O ARG M 213 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG M 213 " --> pdb=" O SER M 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR M 214 " --> pdb=" O ARG M 226 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR M 224 " --> pdb=" O MET M 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 423 through 424 removed outlier: 4.192A pdb=" N ARG M 433 " --> pdb=" O TRP M 424 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 454 through 456 Processing sheet with id=AC9, first strand: chain 'M' and resid 540 through 541 removed outlier: 5.532A pdb=" N PHE M 540 " --> pdb=" O ILE M 585 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 630 through 633 removed outlier: 3.696A pdb=" N ARG M 594 " --> pdb=" O LEU M 633 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 720 through 721 Processing sheet with id=AD3, first strand: chain 'M' and resid 927 through 929 removed outlier: 8.569A pdb=" N ILE M 927 " --> pdb=" O ASN M 738 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR M 740 " --> pdb=" O ILE M 927 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N MET M 929 " --> pdb=" O THR M 740 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA M 742 " --> pdb=" O MET M 929 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 754 through 755 Processing sheet with id=AD5, first strand: chain 'M' and resid 865 through 870 removed outlier: 6.139A pdb=" N LEU M 884 " --> pdb=" O GLU M 867 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL M 869 " --> pdb=" O LYS M 882 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS M 882 " --> pdb=" O VAL M 869 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 986 through 987 Processing sheet with id=AD7, first strand: chain 'M' and resid 1075 through 1077 removed outlier: 3.619A pdb=" N PHE M1075 " --> pdb=" O ILE M1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 34 through 35 Processing sheet with id=AD9, first strand: chain 'X' and resid 157 through 159 962 hydrogen bonds defined for protein. 2712 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: 11.74 Time building geometry restraints manager: 14.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.62: 34734 1.62 - 2.03: 384 2.03 - 2.44: 0 2.44 - 2.85: 0 2.85 - 3.25: 2 Bond restraints: 35120 Sorted by residual: bond pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " ideal model delta sigma weight residual 1.520 3.254 -1.734 3.00e-02 1.11e+03 3.34e+03 bond pdb=" CD LYS D 146 " pdb=" CE LYS D 146 " ideal model delta sigma weight residual 1.520 3.094 -1.574 3.00e-02 1.11e+03 2.75e+03 bond pdb=" CD1 PHE D 88 " pdb=" CE1 PHE D 88 " ideal model delta sigma weight residual 1.382 1.989 -0.607 3.00e-02 1.11e+03 4.10e+02 bond pdb=" CD2 PHE D 88 " pdb=" CE2 PHE D 88 " ideal model delta sigma weight residual 1.382 1.988 -0.606 3.00e-02 1.11e+03 4.07e+02 bond pdb=" CD2 TYR N 85 " pdb=" CE2 TYR N 85 " ideal model delta sigma weight residual 1.382 1.987 -0.605 3.00e-02 1.11e+03 4.07e+02 ... (remaining 35115 not shown) Histogram of bond angle deviations from ideal: 96.75 - 106.24: 985 106.24 - 115.73: 21986 115.73 - 125.22: 23898 125.22 - 134.72: 526 134.72 - 144.21: 4 Bond angle restraints: 47399 Sorted by residual: angle pdb=" CG LYS D 146 " pdb=" CD LYS D 146 " pdb=" CE LYS D 146 " ideal model delta sigma weight residual 111.30 141.41 -30.11 2.30e+00 1.89e-01 1.71e+02 angle pdb=" CA ARG N 29 " pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " ideal model delta sigma weight residual 114.10 134.80 -20.70 2.00e+00 2.50e-01 1.07e+02 angle pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " pdb=" CD ARG N 29 " ideal model delta sigma weight residual 111.30 134.41 -23.11 2.30e+00 1.89e-01 1.01e+02 angle pdb=" N PRO N 612 " pdb=" CA PRO N 612 " pdb=" CB PRO N 612 " ideal model delta sigma weight residual 103.25 111.90 -8.65 1.05e+00 9.07e-01 6.79e+01 angle pdb=" N PRO N1123 " pdb=" CA PRO N1123 " pdb=" CB PRO N1123 " ideal model delta sigma weight residual 103.34 110.40 -7.06 9.30e-01 1.16e+00 5.77e+01 ... (remaining 47394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 18779 17.78 - 35.56: 2303 35.56 - 53.35: 380 53.35 - 71.13: 49 71.13 - 88.91: 26 Dihedral angle restraints: 21537 sinusoidal: 8755 harmonic: 12782 Sorted by residual: dihedral pdb=" CA ASN N1277 " pdb=" C ASN N1277 " pdb=" N HIS N1278 " pdb=" CA HIS N1278 " ideal model delta harmonic sigma weight residual -180.00 -123.50 -56.50 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA CYS N 960 " pdb=" C CYS N 960 " pdb=" N CYS N 961 " pdb=" CA CYS N 961 " ideal model delta harmonic sigma weight residual -180.00 -124.91 -55.09 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA SER N 776 " pdb=" C SER N 776 " pdb=" N PRO N 777 " pdb=" CA PRO N 777 " ideal model delta harmonic sigma weight residual -180.00 -127.57 -52.43 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 21534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4414 0.070 - 0.140: 863 0.140 - 0.210: 87 0.210 - 0.280: 18 0.280 - 0.350: 3 Chirality restraints: 5385 Sorted by residual: chirality pdb=" CG LEU M 546 " pdb=" CB LEU M 546 " pdb=" CD1 LEU M 546 " pdb=" CD2 LEU M 546 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA LEU M 498 " pdb=" N LEU M 498 " pdb=" C LEU M 498 " pdb=" CB LEU M 498 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA PRO N1162 " pdb=" N PRO N1162 " pdb=" C PRO N1162 " pdb=" CB PRO N1162 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 5382 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG M 594 " 0.086 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO M 595 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO M 595 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO M 595 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 203 " 0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO K 204 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO K 204 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO K 204 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 52 " 0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO F 53 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 53 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 53 " 0.046 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 485 2.51 - 3.11: 28028 3.11 - 3.71: 54757 3.71 - 4.30: 78257 4.30 - 4.90: 122470 Nonbonded interactions: 283997 Sorted by model distance: nonbonded pdb=" SD MET N1275 " pdb=" CE MET N1280 " model vdw 1.913 3.820 nonbonded pdb=" OG1 THR B 9 " pdb=" O CYS M 924 " model vdw 1.962 2.440 nonbonded pdb=" OG SER N 817 " pdb=" O ALA N 830 " model vdw 2.041 2.440 nonbonded pdb=" O ALA H 39 " pdb=" NH2 ARG H 44 " model vdw 2.061 2.520 nonbonded pdb=" OE2 GLU M 726 " pdb=" OH TYR M 960 " model vdw 2.096 2.440 ... (remaining 283992 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.310 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 86.990 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.150 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4599 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 : 0.016 1.734 35120 Z= 1.104 Angle : 1.102 30.109 47399 Z= 0.593 Chirality : 0.056 0.350 5385 Planarity : 0.007 0.133 6096 Dihedral : 15.357 88.910 13241 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 32.62 Ramachandran Plot: Outliers : 0.61 % Allowed : 20.78 % Favored : 78.61 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.72 % Twisted Proline : 3.30 % Twisted General : 1.25 % 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: -4.78 (0.11), residues: 4297 helix: -1.63 (0.13), residues: 1334 sheet: -4.22 (0.27), residues: 231 loop : -4.19 (0.10), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP H 40 HIS 0.014 0.002 HIS M 501 PHE 0.045 0.003 PHE D 88 TYR 0.053 0.003 TYR M 746 ARG 0.014 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 3.849 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: 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: 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: N 307 MET cc_start: 0.0828 (tmm) cc_final: -0.0365 (tmm) REVERT: N 512 THR cc_start: 0.5926 (p) cc_final: 0.5665 (p) REVERT: N 680 MET cc_start: 0.7291 (mtm) cc_final: 0.7053 (mtp) REVERT: N 1023 MET cc_start: 0.6272 (mmm) cc_final: 0.5648 (mpp) REVERT: N 1061 MET cc_start: 0.4169 (ttm) cc_final: 0.2799 (tpt) REVERT: N 1311 MET cc_start: 0.0146 (pmm) cc_final: -0.1444 (mtt) REVERT: N 1317 MET cc_start: 0.2739 (tmm) cc_final: 0.2168 (tpt) REVERT: C 53 VAL cc_start: 0.5778 (t) cc_final: 0.5300 (t) REVERT: D 147 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7281 (pttp) REVERT: H 87 MET cc_start: 0.6655 (mmm) cc_final: 0.6386 (mmm) REVERT: I 52 TYR cc_start: 0.3448 (m-80) cc_final: 0.3212 (m-80) REVERT: J 7 MET cc_start: 0.1231 (ptm) cc_final: 0.0949 (ttp) REVERT: K 107 THR cc_start: 0.4574 (p) cc_final: 0.4255 (t) REVERT: M 136 MET cc_start: 0.5594 (tpp) cc_final: 0.5042 (mmp) REVERT: M 168 TYR cc_start: 0.7229 (p90) cc_final: 0.7016 (p90) REVERT: M 584 TYR cc_start: 0.6672 (m-80) cc_final: 0.6196 (m-80) REVERT: M 723 LYS cc_start: 0.7227 (mttt) cc_final: 0.6895 (tptt) REVERT: M 900 ARG cc_start: 0.7153 (mmt90) cc_final: 0.6760 (mtp180) REVERT: M 904 LYS cc_start: 0.7244 (ptpp) cc_final: 0.6890 (pttp) REVERT: Z 232 MET cc_start: -0.2387 (tmm) cc_final: -0.4179 (tpt) REVERT: X 385 MET cc_start: -0.0501 (ttt) cc_final: -0.3993 (mtt) REVERT: X 474 MET cc_start: -0.2866 (tmm) cc_final: -0.3485 (ttm) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.5784 time to fit residues: 591.3315 Evaluate side-chains 364 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 392 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 ASN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 ASN ** N 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1277 ASN ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 268 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 GLN K 29 GLN M 79 ASN M 208 HIS ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 423 ASN M 475 GLN M 535 ASN M 642 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 738 ASN ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 806 HIS ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 913 GLN M1034 GLN ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.726 35120 Z= 1.082 Angle : 0.966 25.622 47399 Z= 0.489 Chirality : 0.050 0.271 5385 Planarity : 0.007 0.089 6096 Dihedral : 8.570 53.385 4758 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 29.05 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.94 % Favored : 81.57 % Rotamer: Outliers : 2.00 % Allowed : 12.45 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.75 % Twisted Proline : 1.10 % Twisted General : 0.92 % 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: -4.33 (0.11), residues: 4297 helix: -1.29 (0.13), residues: 1350 sheet: -3.76 (0.27), residues: 252 loop : -3.90 (0.10), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP M 297 HIS 0.010 0.001 HIS N1239 PHE 0.036 0.002 PHE M 621 TYR 0.039 0.002 TYR M 674 ARG 0.012 0.001 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 413 time to evaluate : 3.937 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 307 MET cc_start: 0.0099 (tmm) cc_final: -0.0279 (tmm) REVERT: N 1039 GLN cc_start: 0.5376 (OUTLIER) cc_final: 0.4925 (mt0) REVERT: N 1061 MET cc_start: 0.4256 (ttm) cc_final: 0.3160 (tpt) REVERT: N 1311 MET cc_start: 0.0146 (pmm) cc_final: -0.1434 (mtt) REVERT: N 1317 MET cc_start: 0.2823 (tmm) cc_final: 0.2040 (tpt) REVERT: D 147 LYS cc_start: 0.7679 (ttmt) cc_final: 0.6943 (pttp) REVERT: K 107 THR cc_start: 0.4325 (p) cc_final: 0.3910 (t) REVERT: M 744 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6185 (mmm) REVERT: M 746 TYR cc_start: 0.5866 (OUTLIER) cc_final: 0.4704 (m-10) REVERT: Z 232 MET cc_start: -0.2322 (tmm) cc_final: -0.3572 (tpt) REVERT: X 273 MET cc_start: 0.5242 (mmm) cc_final: 0.5039 (mmm) REVERT: X 385 MET cc_start: -0.0044 (ttt) cc_final: -0.3306 (mtt) REVERT: X 474 MET cc_start: -0.2772 (tmm) cc_final: -0.3318 (ttm) outliers start: 75 outliers final: 30 residues processed: 454 average time/residue: 0.5050 time to fit residues: 362.1352 Evaluate side-chains 364 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 331 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1227 VAL Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 268 GLN Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain H residue 334 ARG Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 432 ASP Chi-restraints excluded: chain M residue 475 GLN Chi-restraints excluded: chain M residue 503 THR Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 674 TYR Chi-restraints excluded: chain M residue 744 MET Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 895 ASP Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 1050 MET Chi-restraints excluded: chain X residue 85 MET Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 50.0000 chunk 121 optimal weight: 30.0000 chunk 326 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 393 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 350 optimal weight: 3.9990 chunk 389 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 315 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN N 157 HIS N 182 ASN N 225 ASN ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 802 GLN ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1327 HIS B 52 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 475 GLN ** M 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 959 HIS ** M 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 445 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.733 35120 Z= 1.202 Angle : 1.164 22.936 47399 Z= 0.590 Chirality : 0.057 0.381 5385 Planarity : 0.009 0.123 6096 Dihedral : 9.113 52.132 4758 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 38.54 Ramachandran Plot: Outliers : 0.72 % Allowed : 20.67 % Favored : 78.61 % Rotamer: Outliers : 4.17 % Allowed : 17.74 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.77 % Twisted Proline : 1.10 % Twisted General : 0.99 % 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: -4.47 (0.11), residues: 4297 helix: -1.43 (0.13), residues: 1359 sheet: -3.71 (0.27), residues: 272 loop : -3.99 (0.10), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 40 HIS 0.017 0.002 HIS M 676 PHE 0.055 0.003 PHE M 91 TYR 0.044 0.003 TYR M 746 ARG 0.010 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 347 time to evaluate : 3.937 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 674 ASN cc_start: 0.6424 (OUTLIER) cc_final: 0.6116 (t0) REVERT: N 813 PHE cc_start: 0.5306 (OUTLIER) cc_final: 0.3655 (m-80) REVERT: N 1023 MET cc_start: 0.6883 (mmt) cc_final: 0.6532 (mmp) REVERT: N 1039 GLN cc_start: 0.5425 (OUTLIER) cc_final: 0.4697 (mp10) REVERT: N 1280 MET cc_start: 0.4295 (OUTLIER) cc_final: 0.4067 (ptp) REVERT: N 1311 MET cc_start: 0.0187 (pmm) cc_final: -0.1802 (mtt) REVERT: N 1317 MET cc_start: 0.3053 (tmm) cc_final: 0.2343 (tpt) REVERT: B 42 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7354 (mtt180) REVERT: H 230 THR cc_start: 0.6945 (p) cc_final: 0.6626 (p) REVERT: H 233 TYR cc_start: 0.7536 (m-80) cc_final: 0.5735 (m-80) REVERT: H 285 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7255 (ttp80) REVERT: J 76 VAL cc_start: 0.4198 (OUTLIER) cc_final: 0.2341 (m) REVERT: M 498 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6743 (tt) REVERT: M 621 PHE cc_start: 0.3954 (OUTLIER) cc_final: 0.3391 (t80) REVERT: M 676 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6674 (m-70) REVERT: M 692 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: M 746 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5609 (m-10) REVERT: M 979 HIS cc_start: 0.5967 (OUTLIER) cc_final: 0.4962 (m90) REVERT: M 1018 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: Z 232 MET cc_start: -0.2225 (tmm) cc_final: -0.3025 (tpt) REVERT: X 385 MET cc_start: 0.0029 (ttt) cc_final: -0.3587 (mtt) REVERT: X 474 MET cc_start: -0.3112 (tmm) cc_final: -0.3543 (ttm) outliers start: 156 outliers final: 80 residues processed: 475 average time/residue: 0.4778 time to fit residues: 368.6861 Evaluate side-chains 390 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 297 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 479 ARG Chi-restraints excluded: chain N residue 560 ASP Chi-restraints excluded: chain N residue 674 ASN Chi-restraints excluded: chain N residue 694 ARG Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 792 ILE Chi-restraints excluded: chain N residue 811 ASP Chi-restraints excluded: chain N residue 813 PHE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain H residue 327 LYS Chi-restraints excluded: chain H residue 334 ARG Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 432 ASP Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 561 LEU Chi-restraints excluded: chain M residue 621 PHE Chi-restraints excluded: chain M residue 635 VAL Chi-restraints excluded: chain M residue 663 THR Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 674 TYR Chi-restraints excluded: chain M residue 676 HIS Chi-restraints excluded: chain M residue 689 MET Chi-restraints excluded: chain M residue 692 GLN Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 853 ASP Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 888 THR Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 958 PHE Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1018 ASP Chi-restraints excluded: chain X residue 85 MET Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 263 optimal weight: 6.9990 chunk 394 optimal weight: 30.0000 chunk 417 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 373 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 927 ASN ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 608 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1121 ASN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5085 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.727 35120 Z= 1.121 Angle : 0.990 23.766 47399 Z= 0.502 Chirality : 0.052 0.286 5385 Planarity : 0.007 0.084 6096 Dihedral : 8.574 50.984 4758 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 33.18 Ramachandran Plot: Outliers : 0.51 % Allowed : 18.78 % Favored : 80.71 % Rotamer: Outliers : 4.49 % Allowed : 20.35 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.65 % Twisted General : 0.82 % 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: -4.31 (0.12), residues: 4297 helix: -1.27 (0.13), residues: 1367 sheet: -3.73 (0.26), residues: 288 loop : -3.90 (0.10), residues: 2642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 297 HIS 0.018 0.002 HIS M 676 PHE 0.048 0.003 PHE M 91 TYR 0.042 0.003 TYR M1088 ARG 0.011 0.001 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 329 time to evaluate : 4.331 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 599 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: N 674 ASN cc_start: 0.6546 (t0) cc_final: 0.6285 (t0) REVERT: N 694 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7207 (ttp80) REVERT: N 717 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5795 (mp) REVERT: N 731 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6724 (tt) REVERT: N 813 PHE cc_start: 0.4888 (OUTLIER) cc_final: 0.3284 (m-80) REVERT: N 1023 MET cc_start: 0.6796 (mmt) cc_final: 0.6381 (mmp) REVERT: N 1039 GLN cc_start: 0.5468 (OUTLIER) cc_final: 0.4772 (mp10) REVERT: N 1311 MET cc_start: 0.0026 (pmm) cc_final: -0.1932 (mtt) REVERT: N 1317 MET cc_start: 0.3147 (tmm) cc_final: 0.2480 (tpt) REVERT: D 137 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7908 (t) REVERT: F 133 GLN cc_start: 0.5348 (OUTLIER) cc_final: 0.4825 (mm-40) REVERT: H 233 TYR cc_start: 0.7268 (m-80) cc_final: 0.5378 (m-80) REVERT: H 285 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7294 (ttp80) REVERT: K 64 THR cc_start: 0.5905 (OUTLIER) cc_final: 0.5669 (m) REVERT: M 47 PHE cc_start: 0.7495 (t80) cc_final: 0.7126 (t80) REVERT: M 692 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: M 706 ASP cc_start: 0.7941 (t70) cc_final: 0.7703 (t0) REVERT: M 977 VAL cc_start: 0.7469 (t) cc_final: 0.7182 (t) REVERT: M 979 HIS cc_start: 0.5716 (OUTLIER) cc_final: 0.4707 (m90) REVERT: M 1003 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6889 (t80) REVERT: M 1004 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8003 (t80) REVERT: M 1069 MET cc_start: 0.6302 (ppp) cc_final: 0.5925 (ppp) REVERT: Z 232 MET cc_start: -0.2338 (tmm) cc_final: -0.2999 (tpt) REVERT: X 385 MET cc_start: -0.0025 (ttt) cc_final: -0.3730 (mtt) REVERT: X 474 MET cc_start: -0.3490 (tmm) cc_final: -0.3821 (ttm) outliers start: 168 outliers final: 82 residues processed: 475 average time/residue: 0.4636 time to fit residues: 359.9661 Evaluate side-chains 393 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 298 time to evaluate : 3.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 370 SER Chi-restraints excluded: chain N residue 479 ARG Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 599 GLN Chi-restraints excluded: chain N residue 694 ARG Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 717 LEU Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 768 LEU Chi-restraints excluded: chain N residue 813 PHE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 878 SER Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1084 ILE Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1301 LEU Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain H residue 334 ARG Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 228 ASN Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 432 ASP Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 561 LEU Chi-restraints excluded: chain M residue 663 THR Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 689 MET Chi-restraints excluded: chain M residue 692 GLN Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 783 THR Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 904 LYS Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 969 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 1003 TYR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 85 MET Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 310 optimal weight: 0.6980 chunk 172 optimal weight: 20.0000 chunk 356 optimal weight: 0.9980 chunk 288 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 213 optimal weight: 0.6980 chunk 374 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 358 GLN M 79 ASN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 982 ASN M1021 HIS ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN X 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4940 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.722 35120 Z= 1.073 Angle : 0.891 23.744 47399 Z= 0.448 Chirality : 0.048 0.273 5385 Planarity : 0.006 0.086 6096 Dihedral : 7.951 50.826 4758 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 28.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 17.78 % Favored : 81.87 % Rotamer: Outliers : 3.71 % Allowed : 22.73 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.65 % Twisted General : 0.58 % 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: -4.03 (0.12), residues: 4297 helix: -0.98 (0.14), residues: 1366 sheet: -3.67 (0.25), residues: 311 loop : -3.73 (0.11), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 297 HIS 0.027 0.001 HIS G 45 PHE 0.050 0.002 PHE M 377 TYR 0.024 0.002 TYR M 746 ARG 0.006 0.001 ARG X 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 348 time to evaluate : 4.002 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 694 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7231 (ttp80) REVERT: N 731 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6572 (tt) REVERT: N 789 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6128 (m-10) REVERT: N 852 MET cc_start: 0.6718 (mtp) cc_final: 0.6185 (mtp) REVERT: N 1023 MET cc_start: 0.6840 (mmt) cc_final: 0.6323 (mmp) REVERT: N 1039 GLN cc_start: 0.5207 (OUTLIER) cc_final: 0.4608 (mp10) REVERT: N 1311 MET cc_start: -0.0185 (pmm) cc_final: -0.2059 (mtt) REVERT: N 1317 MET cc_start: 0.3170 (tmm) cc_final: 0.2465 (tpt) REVERT: F 133 GLN cc_start: 0.5362 (OUTLIER) cc_final: 0.4872 (mm-40) REVERT: H 169 TYR cc_start: 0.8021 (m-80) cc_final: 0.7789 (m-80) REVERT: H 202 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8103 (mp) REVERT: H 330 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: M 47 PHE cc_start: 0.7342 (t80) cc_final: 0.6893 (t80) REVERT: M 164 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.7065 (p0) REVERT: M 979 HIS cc_start: 0.5892 (OUTLIER) cc_final: 0.4996 (m90) REVERT: Z 232 MET cc_start: -0.2120 (tmm) cc_final: -0.2778 (tpt) REVERT: X 385 MET cc_start: 0.0816 (ttt) cc_final: -0.3820 (mtt) outliers start: 139 outliers final: 71 residues processed: 462 average time/residue: 0.4588 time to fit residues: 346.4840 Evaluate side-chains 380 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 300 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 592 VAL Chi-restraints excluded: chain N residue 640 ILE Chi-restraints excluded: chain N residue 694 ARG Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 789 PHE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 953 MET Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1301 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 499 MET Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 648 HIS Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 804 TRP Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 904 LYS Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 990 THR Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 85 MET Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.0470 chunk 376 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 417 optimal weight: 20.0000 chunk 346 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 138 optimal weight: 3.9990 chunk 219 optimal weight: 50.0000 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 HIS ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 577 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.723 35120 Z= 1.096 Angle : 0.932 23.315 47399 Z= 0.469 Chirality : 0.050 0.329 5385 Planarity : 0.006 0.080 6096 Dihedral : 7.970 51.059 4758 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 30.98 Ramachandran Plot: Outliers : 0.37 % Allowed : 19.01 % Favored : 80.61 % Rotamer: Outliers : 4.89 % Allowed : 22.60 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.51 % 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: -3.97 (0.12), residues: 4297 helix: -0.90 (0.14), residues: 1378 sheet: -3.73 (0.25), residues: 318 loop : -3.72 (0.11), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 73 HIS 0.009 0.001 HIS M 676 PHE 0.049 0.002 PHE M 377 TYR 0.032 0.002 TYR M 746 ARG 0.017 0.001 ARG N 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 320 time to evaluate : 4.121 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: 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: symmetry clash REVERT: N 599 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: N 694 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7306 (ttp80) REVERT: N 731 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6593 (tt) REVERT: N 789 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6367 (m-10) REVERT: N 813 PHE cc_start: 0.4591 (OUTLIER) cc_final: 0.3004 (m-80) REVERT: N 1023 MET cc_start: 0.6749 (mmt) cc_final: 0.6225 (mmp) REVERT: N 1039 GLN cc_start: 0.5207 (OUTLIER) cc_final: 0.4373 (mp10) REVERT: N 1311 MET cc_start: -0.0047 (pmm) cc_final: -0.2010 (mtt) REVERT: N 1317 MET cc_start: 0.3177 (tmm) cc_final: 0.2457 (tpt) REVERT: F 133 GLN cc_start: 0.5683 (OUTLIER) cc_final: 0.5036 (mm-40) REVERT: H 202 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8059 (mp) REVERT: H 285 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7169 (ttp80) REVERT: H 330 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7485 (mtm) REVERT: J 125 GLN cc_start: 0.5829 (mp10) cc_final: 0.5431 (mp10) REVERT: M 47 PHE cc_start: 0.7443 (t80) cc_final: 0.7126 (t80) REVERT: M 164 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7253 (p0) REVERT: M 692 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6634 (pt0) REVERT: M 979 HIS cc_start: 0.5783 (OUTLIER) cc_final: 0.4810 (m90) REVERT: M 1003 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6642 (t80) REVERT: M 1004 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8106 (t80) REVERT: M 1010 GLN cc_start: 0.7767 (mp10) cc_final: 0.7474 (mp10) REVERT: Z 232 MET cc_start: -0.2101 (tmm) cc_final: -0.2836 (tpt) REVERT: X 130 THR cc_start: 0.2231 (OUTLIER) cc_final: 0.2020 (p) REVERT: X 385 MET cc_start: 0.0188 (ttt) cc_final: -0.4196 (mtt) REVERT: X 474 MET cc_start: -0.3769 (tmm) cc_final: -0.4018 (ttm) outliers start: 183 outliers final: 107 residues processed: 476 average time/residue: 0.4536 time to fit residues: 354.3328 Evaluate side-chains 419 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 297 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 370 SER Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 560 ASP Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 592 VAL Chi-restraints excluded: chain N residue 599 GLN Chi-restraints excluded: chain N residue 694 ARG Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 725 ASP Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 788 SER Chi-restraints excluded: chain N residue 789 PHE Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 813 PHE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 878 SER Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 953 MET Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1040 SER Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1084 ILE Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1230 ASP Chi-restraints excluded: chain N residue 1329 PHE Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain L residue 347 ASP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 480 CYS Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 499 MET Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 648 HIS Chi-restraints excluded: chain M residue 692 GLN Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 755 LEU Chi-restraints excluded: chain M residue 759 LYS Chi-restraints excluded: chain M residue 783 THR Chi-restraints excluded: chain M residue 804 TRP Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 853 ASP Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 904 LYS Chi-restraints excluded: chain M residue 909 LEU Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 958 PHE Chi-restraints excluded: chain M residue 964 PHE Chi-restraints excluded: chain M residue 969 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 990 THR Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1003 TYR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain M residue 1016 VAL Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 41 HIS Chi-restraints excluded: chain X residue 85 MET Chi-restraints excluded: chain X residue 130 THR Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 238 optimal weight: 40.0000 chunk 305 optimal weight: 30.0000 chunk 236 optimal weight: 0.0070 chunk 351 optimal weight: 4.9990 chunk 233 optimal weight: 30.0000 chunk 416 optimal weight: 0.0170 chunk 260 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 217 ASN N 314 GLN ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 674 ASN ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 180 ASN H 305 HIS ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 848 GLN ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 507 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.722 35120 Z= 1.078 Angle : 0.891 23.254 47399 Z= 0.447 Chirality : 0.048 0.319 5385 Planarity : 0.006 0.078 6096 Dihedral : 7.660 50.157 4758 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 17.22 % Favored : 82.38 % Rotamer: Outliers : 4.25 % Allowed : 23.88 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.43 % 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: -3.89 (0.12), residues: 4297 helix: -0.83 (0.14), residues: 1385 sheet: -3.64 (0.24), residues: 353 loop : -3.66 (0.11), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 297 HIS 0.010 0.001 HIS M 676 PHE 0.053 0.002 PHE M 377 TYR 0.025 0.002 TYR M 746 ARG 0.016 0.001 ARG N 923 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 326 time to evaluate : 4.075 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 107 MET cc_start: 0.4343 (mpp) cc_final: 0.3978 (mpp) REVERT: N 117 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.4342 (mm) REVERT: N 599 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: N 731 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6307 (tt) REVERT: N 789 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6198 (m-10) REVERT: N 813 PHE cc_start: 0.4326 (OUTLIER) cc_final: 0.2985 (m-80) REVERT: N 852 MET cc_start: 0.6652 (mtp) cc_final: 0.6169 (mtp) REVERT: N 1023 MET cc_start: 0.6349 (mmt) cc_final: 0.5910 (mmp) REVERT: N 1039 GLN cc_start: 0.5193 (OUTLIER) cc_final: 0.4299 (mp10) REVERT: N 1311 MET cc_start: -0.0166 (pmm) cc_final: -0.2187 (mtt) REVERT: N 1317 MET cc_start: 0.2883 (tmm) cc_final: 0.2189 (tpt) REVERT: D 20 LYS cc_start: 0.6557 (mmmt) cc_final: 0.6058 (mmmt) REVERT: D 92 MET cc_start: 0.5726 (tmm) cc_final: 0.5222 (tmm) REVERT: D 140 ARG cc_start: 0.4111 (ttm-80) cc_final: 0.2707 (mtt90) REVERT: F 133 GLN cc_start: 0.5716 (OUTLIER) cc_final: 0.4966 (mm-40) REVERT: H 198 LEU cc_start: 0.5922 (tp) cc_final: 0.5623 (tp) REVERT: H 202 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8045 (mp) REVERT: H 289 ARG cc_start: 0.3778 (mtt-85) cc_final: 0.3560 (mmt90) REVERT: H 330 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7415 (mtm) REVERT: M 47 PHE cc_start: 0.7324 (t80) cc_final: 0.7098 (t80) REVERT: M 164 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.7042 (p0) REVERT: M 172 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6409 (mmmt) REVERT: M 377 PHE cc_start: 0.4392 (m-80) cc_final: 0.3270 (m-80) REVERT: M 692 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6670 (pt0) REVERT: M 870 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7366 (tmm) REVERT: M 979 HIS cc_start: 0.5917 (OUTLIER) cc_final: 0.5088 (m90) REVERT: M 1003 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6266 (t80) REVERT: M 1004 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7882 (t80) REVERT: Z 232 MET cc_start: -0.2176 (tmm) cc_final: -0.2897 (tpt) REVERT: X 130 THR cc_start: 0.2197 (OUTLIER) cc_final: 0.1985 (p) REVERT: X 340 LYS cc_start: 0.2448 (OUTLIER) cc_final: 0.2042 (tptt) REVERT: X 385 MET cc_start: 0.0208 (ttt) cc_final: -0.4390 (mtt) REVERT: X 434 MET cc_start: -0.1056 (ttp) cc_final: -0.1471 (ttp) REVERT: X 474 MET cc_start: -0.3827 (tmm) cc_final: -0.4042 (ttm) outliers start: 159 outliers final: 94 residues processed: 457 average time/residue: 0.4957 time to fit residues: 373.6842 Evaluate side-chains 414 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 302 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 370 SER Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 507 LEU Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 592 VAL Chi-restraints excluded: chain N residue 599 GLN Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 700 ILE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 788 SER Chi-restraints excluded: chain N residue 789 PHE Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 813 PHE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1040 SER Chi-restraints excluded: chain N residue 1048 MET Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1230 ASP Chi-restraints excluded: chain N residue 1301 LEU Chi-restraints excluded: chain N residue 1329 PHE Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 161 CYS Chi-restraints excluded: chain M residue 164 ASP Chi-restraints excluded: chain M residue 172 LYS Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 441 SER Chi-restraints excluded: chain M residue 480 CYS Chi-restraints excluded: chain M residue 495 ASN Chi-restraints excluded: chain M residue 502 ILE Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 648 HIS Chi-restraints excluded: chain M residue 692 GLN Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 755 LEU Chi-restraints excluded: chain M residue 759 LYS Chi-restraints excluded: chain M residue 804 TRP Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 853 ASP Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 870 MET Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 990 THR Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1003 TYR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain M residue 1086 LEU Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 130 THR Chi-restraints excluded: chain X residue 340 LYS Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 125 optimal weight: 40.0000 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 264 optimal weight: 0.3980 chunk 283 optimal weight: 0.0270 chunk 205 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 327 optimal weight: 5.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 674 ASN ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN H 180 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 381 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4887 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.720 35120 Z= 1.070 Angle : 0.870 23.043 47399 Z= 0.435 Chirality : 0.048 0.276 5385 Planarity : 0.006 0.078 6096 Dihedral : 7.343 49.884 4758 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 26.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.62 % Favored : 83.03 % Rotamer: Outliers : 3.55 % Allowed : 24.73 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.31 % 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: -3.74 (0.12), residues: 4297 helix: -0.72 (0.14), residues: 1383 sheet: -3.60 (0.23), residues: 354 loop : -3.55 (0.11), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 297 HIS 0.012 0.001 HIS M 501 PHE 0.048 0.002 PHE M 377 TYR 0.021 0.002 TYR M 746 ARG 0.016 0.001 ARG N 923 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 329 time to evaluate : 4.239 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: 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: symmetry clash REVERT: N 107 MET cc_start: 0.4270 (mpp) cc_final: 0.3917 (mpp) REVERT: N 281 MET cc_start: 0.3575 (mmp) cc_final: 0.3255 (mmm) REVERT: N 370 SER cc_start: 0.5812 (OUTLIER) cc_final: 0.5537 (p) REVERT: N 731 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6261 (tt) REVERT: N 789 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.5942 (m-10) REVERT: N 852 MET cc_start: 0.6671 (mtp) cc_final: 0.6172 (mtp) REVERT: N 1023 MET cc_start: 0.6165 (mmt) cc_final: 0.5569 (mmp) REVERT: N 1039 GLN cc_start: 0.5242 (OUTLIER) cc_final: 0.4396 (mp10) REVERT: N 1311 MET cc_start: -0.0166 (pmm) cc_final: -0.2165 (mtt) REVERT: N 1317 MET cc_start: 0.2898 (tmm) cc_final: 0.2157 (tpt) REVERT: D 20 LYS cc_start: 0.6498 (mmmt) cc_final: 0.6174 (mmmt) REVERT: D 92 MET cc_start: 0.5764 (tmm) cc_final: 0.5290 (tmm) REVERT: F 133 GLN cc_start: 0.5583 (OUTLIER) cc_final: 0.4932 (mm-40) REVERT: H 10 MET cc_start: 0.6118 (ppp) cc_final: 0.5439 (ppp) REVERT: H 202 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8052 (mp) REVERT: H 330 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7380 (mtm) REVERT: M 172 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6251 (mmmt) REVERT: M 711 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8801 (tt) REVERT: M 870 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7353 (tmm) REVERT: M 904 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.5624 (pttm) REVERT: M 979 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.5032 (m90) REVERT: M 1004 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7961 (t80) REVERT: M 1069 MET cc_start: 0.6748 (ppp) cc_final: 0.6406 (ppp) REVERT: Z 232 MET cc_start: -0.2228 (tmm) cc_final: -0.2942 (tpt) REVERT: X 130 THR cc_start: 0.1990 (OUTLIER) cc_final: 0.1789 (p) REVERT: X 385 MET cc_start: 0.0274 (ttt) cc_final: -0.4492 (mtt) REVERT: X 434 MET cc_start: -0.0910 (ttp) cc_final: -0.1294 (ttp) REVERT: X 531 MET cc_start: 0.2131 (mmm) cc_final: 0.1615 (tpt) outliers start: 133 outliers final: 92 residues processed: 440 average time/residue: 0.4525 time to fit residues: 326.4142 Evaluate side-chains 406 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 300 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 370 SER Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 560 ASP Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 592 VAL Chi-restraints excluded: chain N residue 640 ILE Chi-restraints excluded: chain N residue 674 ASN Chi-restraints excluded: chain N residue 694 ARG Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 700 ILE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 788 SER Chi-restraints excluded: chain N residue 789 PHE Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1040 SER Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1230 ASP Chi-restraints excluded: chain N residue 1301 LEU Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 161 CYS Chi-restraints excluded: chain M residue 172 LYS Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 441 SER Chi-restraints excluded: chain M residue 449 LEU Chi-restraints excluded: chain M residue 480 CYS Chi-restraints excluded: chain M residue 502 ILE Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 648 HIS Chi-restraints excluded: chain M residue 711 LEU Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 755 LEU Chi-restraints excluded: chain M residue 759 LYS Chi-restraints excluded: chain M residue 804 TRP Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 869 VAL Chi-restraints excluded: chain M residue 870 MET Chi-restraints excluded: chain M residue 904 LYS Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 990 THR Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain M residue 1086 LEU Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 41 HIS Chi-restraints excluded: chain X residue 130 THR Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 50.0000 chunk 398 optimal weight: 40.0000 chunk 363 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 233 optimal weight: 40.0000 chunk 169 optimal weight: 0.6980 chunk 304 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 350 optimal weight: 0.1980 chunk 366 optimal weight: 0.7980 chunk 386 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 674 ASN ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN D 46 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN K 110 ASN M 52 ASN ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 848 GLN ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4917 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.721 35120 Z= 1.074 Angle : 0.877 23.097 47399 Z= 0.437 Chirality : 0.048 0.279 5385 Planarity : 0.006 0.079 6096 Dihedral : 7.307 49.890 4758 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.62 % Favored : 83.03 % Rotamer: Outliers : 3.55 % Allowed : 25.16 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.29 % 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: -3.66 (0.12), residues: 4297 helix: -0.65 (0.14), residues: 1387 sheet: -3.48 (0.23), residues: 367 loop : -3.51 (0.11), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 297 HIS 0.007 0.001 HIS N1239 PHE 0.043 0.002 PHE M 377 TYR 0.024 0.002 TYR M 746 ARG 0.011 0.000 ARG N 923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 319 time to evaluate : 4.337 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: 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: N 107 MET cc_start: 0.4421 (mpp) cc_final: 0.4053 (mpp) REVERT: N 281 MET cc_start: 0.3535 (mmp) cc_final: 0.3227 (mmm) REVERT: N 680 MET cc_start: 0.6723 (mtm) cc_final: 0.6450 (mtm) REVERT: N 731 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6409 (tt) REVERT: N 789 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.5922 (m-10) REVERT: N 813 PHE cc_start: 0.4126 (OUTLIER) cc_final: 0.2707 (m-80) REVERT: N 1023 MET cc_start: 0.6036 (mmt) cc_final: 0.5639 (mmp) REVERT: N 1039 GLN cc_start: 0.5468 (OUTLIER) cc_final: 0.4597 (mp10) REVERT: N 1311 MET cc_start: -0.0259 (pmm) cc_final: -0.2210 (mtt) REVERT: N 1317 MET cc_start: 0.2892 (tmm) cc_final: 0.2135 (tpt) REVERT: B 1 MET cc_start: 0.6501 (ttt) cc_final: 0.6148 (ttp) REVERT: D 20 LYS cc_start: 0.6535 (mmmt) cc_final: 0.6251 (mmmt) REVERT: F 133 GLN cc_start: 0.5811 (OUTLIER) cc_final: 0.5106 (mm-40) REVERT: H 10 MET cc_start: 0.6155 (ppp) cc_final: 0.5635 (ppp) REVERT: H 202 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7977 (mp) REVERT: H 289 ARG cc_start: 0.3764 (mmt90) cc_final: 0.3336 (mmt90) REVERT: H 330 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7405 (mtm) REVERT: M 172 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6304 (mmmt) REVERT: M 870 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7418 (tmm) REVERT: M 904 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5667 (pttm) REVERT: M 979 HIS cc_start: 0.5874 (OUTLIER) cc_final: 0.5194 (m90) REVERT: M 1004 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8052 (t80) REVERT: M 1069 MET cc_start: 0.7047 (ppp) cc_final: 0.6578 (ppp) REVERT: Z 232 MET cc_start: -0.2207 (tmm) cc_final: -0.3230 (tpt) REVERT: X 130 THR cc_start: 0.1920 (OUTLIER) cc_final: 0.1636 (p) REVERT: X 385 MET cc_start: 0.0215 (ttt) cc_final: -0.4646 (mtt) REVERT: X 434 MET cc_start: -0.0867 (ttp) cc_final: -0.1246 (ttp) REVERT: X 531 MET cc_start: 0.2153 (mmm) cc_final: 0.1613 (tpt) outliers start: 133 outliers final: 93 residues processed: 431 average time/residue: 0.4500 time to fit residues: 319.7303 Evaluate side-chains 410 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 304 time to evaluate : 4.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 592 VAL Chi-restraints excluded: chain N residue 640 ILE Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 700 ILE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 788 SER Chi-restraints excluded: chain N residue 789 PHE Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 813 PHE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 878 SER Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1040 SER Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1230 ASP Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 100 HIS Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 161 CYS Chi-restraints excluded: chain M residue 172 LYS Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain M residue 441 SER Chi-restraints excluded: chain M residue 449 LEU Chi-restraints excluded: chain M residue 480 CYS Chi-restraints excluded: chain M residue 502 ILE Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 648 HIS Chi-restraints excluded: chain M residue 663 THR Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 755 LEU Chi-restraints excluded: chain M residue 804 TRP Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 853 ASP Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 870 MET Chi-restraints excluded: chain M residue 904 LYS Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 972 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 990 THR Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain M residue 1086 LEU Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 41 HIS Chi-restraints excluded: chain X residue 130 THR Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 9.9990 chunk 410 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 430 optimal weight: 40.0000 chunk 396 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 210 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 290 ASN ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 476 HIS N 528 ASN N 662 ASN ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1026 GLN N1054 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 ASN M 52 ASN ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5154 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.720 35120 Z= 1.141 Angle : 1.028 22.324 47399 Z= 0.517 Chirality : 0.053 0.352 5385 Planarity : 0.007 0.088 6096 Dihedral : 8.000 50.992 4758 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 33.50 Ramachandran Plot: Outliers : 0.37 % Allowed : 19.39 % Favored : 80.24 % Rotamer: Outliers : 3.66 % Allowed : 25.16 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.43 % 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: -3.92 (0.12), residues: 4297 helix: -0.87 (0.14), residues: 1387 sheet: -3.55 (0.24), residues: 325 loop : -3.70 (0.11), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 40 HIS 0.018 0.002 HIS M 676 PHE 0.063 0.003 PHE M 91 TYR 0.043 0.003 TYR M 746 ARG 0.013 0.001 ARG N 923 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 300 time to evaluate : 4.319 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: 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: symmetry clash REVERT: N 107 MET cc_start: 0.4480 (mpp) cc_final: 0.4101 (mpp) REVERT: N 281 MET cc_start: 0.3479 (mmp) cc_final: 0.3095 (mmm) REVERT: N 468 LEU cc_start: 0.7076 (mm) cc_final: 0.6537 (mt) REVERT: N 731 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6478 (tt) REVERT: N 789 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6266 (m-10) REVERT: N 813 PHE cc_start: 0.4936 (OUTLIER) cc_final: 0.3432 (m-80) REVERT: N 1023 MET cc_start: 0.6171 (mmt) cc_final: 0.5671 (mmp) REVERT: N 1039 GLN cc_start: 0.5847 (OUTLIER) cc_final: 0.4916 (mp10) REVERT: N 1311 MET cc_start: 0.0179 (pmm) cc_final: -0.2059 (mtt) REVERT: N 1317 MET cc_start: 0.3273 (tmm) cc_final: 0.2416 (tpt) REVERT: C 48 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7323 (ptm-80) REVERT: D 20 LYS cc_start: 0.6688 (mmmt) cc_final: 0.6365 (mmmt) REVERT: D 126 GLN cc_start: 0.5178 (OUTLIER) cc_final: 0.4519 (mt0) REVERT: H 10 MET cc_start: 0.6405 (ppp) cc_final: 0.5984 (ppp) REVERT: H 202 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7986 (mp) REVERT: H 330 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7310 (mtm) REVERT: M 172 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6668 (mmmt) REVERT: M 692 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: M 870 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.6925 (tmm) REVERT: M 979 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.4897 (m90) REVERT: M 1003 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6233 (t80) REVERT: M 1004 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8017 (t80) REVERT: M 1069 MET cc_start: 0.7017 (ppp) cc_final: 0.6600 (ppp) REVERT: Z 232 MET cc_start: -0.2253 (tmm) cc_final: -0.2961 (tpt) REVERT: X 130 THR cc_start: 0.1974 (OUTLIER) cc_final: 0.1660 (p) REVERT: X 385 MET cc_start: 0.0203 (ttt) cc_final: -0.4267 (mtm) REVERT: X 434 MET cc_start: -0.1061 (ttp) cc_final: -0.1429 (ttp) REVERT: X 531 MET cc_start: 0.2377 (mmm) cc_final: 0.1535 (tpt) outliers start: 137 outliers final: 101 residues processed: 417 average time/residue: 0.4474 time to fit residues: 309.4003 Evaluate side-chains 399 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 283 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 314 GLN Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 592 VAL Chi-restraints excluded: chain N residue 694 ARG Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 700 ILE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 788 SER Chi-restraints excluded: chain N residue 789 PHE Chi-restraints excluded: chain N residue 790 ILE Chi-restraints excluded: chain N residue 813 PHE Chi-restraints excluded: chain N residue 851 THR Chi-restraints excluded: chain N residue 878 SER Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1040 SER Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1230 ASP Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 146 CYS Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 100 HIS Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 161 CYS Chi-restraints excluded: chain M residue 172 LYS Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 441 SER Chi-restraints excluded: chain M residue 449 LEU Chi-restraints excluded: chain M residue 480 CYS Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 648 HIS Chi-restraints excluded: chain M residue 653 ASP Chi-restraints excluded: chain M residue 663 THR Chi-restraints excluded: chain M residue 692 GLN Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 755 LEU Chi-restraints excluded: chain M residue 759 LYS Chi-restraints excluded: chain M residue 804 TRP Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 853 ASP Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 870 MET Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 969 VAL Chi-restraints excluded: chain M residue 972 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 990 THR Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1003 TYR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 41 HIS Chi-restraints excluded: chain X residue 130 THR Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 104 optimal weight: 40.0000 chunk 316 optimal weight: 2.9990 chunk 50 optimal weight: 0.0070 chunk 95 optimal weight: 2.9990 chunk 343 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 352 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 63 optimal weight: 9.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 290 ASN ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 674 ASN ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN H 180 ASN M 52 ASN ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 703 ASN ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.164257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.161148 restraints weight = 84496.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.160819 restraints weight = 154746.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.160438 restraints weight = 159567.563| |-----------------------------------------------------------------------------| r_work (final): 0.4793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4940 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.723 35120 Z= 1.073 Angle : 0.912 22.604 47399 Z= 0.454 Chirality : 0.049 0.276 5385 Planarity : 0.006 0.082 6096 Dihedral : 7.487 51.662 4758 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 26.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.76 % Favored : 83.90 % Rotamer: Outliers : 2.67 % Allowed : 26.36 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.39 % 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: -3.72 (0.12), residues: 4297 helix: -0.69 (0.14), residues: 1380 sheet: -3.51 (0.23), residues: 362 loop : -3.55 (0.11), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 297 HIS 0.012 0.001 HIS N 58 PHE 0.055 0.002 PHE M 377 TYR 0.029 0.002 TYR M1088 ARG 0.016 0.001 ARG D 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7108.73 seconds wall clock time: 130 minutes 10.07 seconds (7810.07 seconds total)