Starting phenix.real_space_refine on Sat Dec 9 17:03:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ceb_7463/12_2023/6ceb_7463_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ceb_7463/12_2023/6ceb_7463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ceb_7463/12_2023/6ceb_7463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ceb_7463/12_2023/6ceb_7463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ceb_7463/12_2023/6ceb_7463_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ceb_7463/12_2023/6ceb_7463_neut.pdb" } resolution = 4.7 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= 0.003 sd= 0.054 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 96 5.16 5 C 7417 2.51 5 N 1969 2.21 5 O 2240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11722 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5500 Classifications: {'peptide': 682} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 645} Chain breaks: 5 Chain: "B" Number of atoms: 4540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4540 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 4 Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "L" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "N" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "P" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.46, per 1000 atoms: 0.55 Number of scatterers: 11722 At special positions: 0 Unit cell: (91.3, 149.6, 154, 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 96 16.00 O 2240 8.00 N 1969 7.00 C 7417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.02 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 11 " distance=2.03 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 11 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG Q 1 " - " NAG Q 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " " NAG G 1 " - " FUC G 2 " " NAG H 1 " - " FUC H 3 " " NAG J 1 " - " FUC J 3 " " NAG R 1 " - " FUC R 2 " NAG-ASN " NAG A1014 " - " ASN A 16 " " NAG B1014 " - " ASN B 16 " " NAG C 1 " - " ASN A 25 " " NAG D 1 " - " ASN A 111 " " NAG E 1 " - " ASN A 255 " " NAG F 1 " - " ASN A 397 " " NAG G 1 " - " ASN A 418 " " NAG H 1 " - " ASN B 25 " " NAG I 1 " - " ASN B 111 " " NAG J 1 " - " ASN B 255 " " NAG Q 1 " - " ASN B 397 " " NAG R 1 " - " ASN B 418 " Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.3 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2656 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 29 sheets defined 17.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.648A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.628A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.592A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 143 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.847A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.834A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.815A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.569A pdb=" N PHE A 642 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 643 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 644 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.741A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.017A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 48' Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.639A pdb=" N ASN B 143 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.759A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.738A pdb=" N ASN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.834A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.528A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'M' and resid 692 through 715 removed outlier: 3.539A pdb=" N LEU M 696 " --> pdb=" O ILE M 692 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU M 709 " --> pdb=" O PHE M 705 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL M 715 " --> pdb=" O ASN M 711 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 12 through 18 removed outlier: 3.792A pdb=" N ASN K 18 " --> pdb=" O TYR K 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 12 through 18 removed outlier: 3.792A pdb=" N ASN N 18 " --> pdb=" O TYR N 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 Processing helix chain 'P' and resid 692 through 715 removed outlier: 3.538A pdb=" N LEU P 696 " --> pdb=" O ILE P 692 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU P 709 " --> pdb=" O PHE P 705 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL P 715 " --> pdb=" O ASN P 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.647A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 4.765A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.607A pdb=" N PHE A 231 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254 removed outlier: 3.514A pdb=" N ARG A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 3.686A pdb=" N LEU A 314 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER A 339 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLU A 316 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N ILE A 341 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N GLU A 318 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AB1, first strand: chain 'A' and resid 402 through 403 removed outlier: 6.452A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.395A pdb=" N GLU A 471 " --> pdb=" O LYS A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.811A pdb=" N LEU A 487 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP A 551 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB6, first strand: chain 'A' and resid 759 through 762 Processing sheet with id=AB7, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.731A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 216 removed outlier: 4.576A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.539A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.525A pdb=" N ARG B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC5, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AC6, first strand: chain 'B' and resid 335 through 336 removed outlier: 3.760A pdb=" N ILE B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AC8, first strand: chain 'B' and resid 402 through 403 removed outlier: 6.622A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.301A pdb=" N GLU B 471 " --> pdb=" O LYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 532 through 534 230 hydrogen bonds defined for protein. 591 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: 3.85 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3729 1.34 - 1.46: 2850 1.46 - 1.58: 5292 1.58 - 1.70: 0 1.70 - 1.83: 115 Bond restraints: 11986 Sorted by residual: bond pdb=" C5 FUC G 2 " pdb=" O5 FUC G 2 " ideal model delta sigma weight residual 1.423 1.471 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C5 FUC R 2 " pdb=" O5 FUC R 2 " ideal model delta sigma weight residual 1.423 1.468 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" CA ASN B 405 " pdb=" CB ASN B 405 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.75e-02 3.27e+03 3.77e+00 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.01: 273 106.01 - 113.01: 6541 113.01 - 120.02: 4129 120.02 - 127.03: 5126 127.03 - 134.04: 165 Bond angle restraints: 16234 Sorted by residual: angle pdb=" C HIS B 1 " pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C HIS A 1 " pdb=" N LEU A 2 " pdb=" CA LEU A 2 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" CA ASP A 591 " pdb=" C ASP A 591 " pdb=" O ASP A 591 " ideal model delta sigma weight residual 117.94 120.79 -2.85 5.80e-01 2.97e+00 2.41e+01 angle pdb=" C ASP A 591 " pdb=" CA ASP A 591 " pdb=" CB ASP A 591 " ideal model delta sigma weight residual 117.07 110.09 6.98 1.44e+00 4.82e-01 2.35e+01 angle pdb=" N GLY B 10 " pdb=" CA GLY B 10 " pdb=" C GLY B 10 " ideal model delta sigma weight residual 110.97 118.48 -7.51 1.56e+00 4.11e-01 2.32e+01 ... (remaining 16229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 7029 15.51 - 31.02: 352 31.02 - 46.53: 101 46.53 - 62.04: 12 62.04 - 77.55: 9 Dihedral angle restraints: 7503 sinusoidal: 3398 harmonic: 4105 Sorted by residual: dihedral pdb=" CA CYS B 468 " pdb=" C CYS B 468 " pdb=" N GLU B 469 " pdb=" CA GLU B 469 " ideal model delta harmonic sigma weight residual 180.00 -133.50 -46.50 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA CYS A 468 " pdb=" C CYS A 468 " pdb=" N GLU A 469 " pdb=" CA GLU A 469 " ideal model delta harmonic sigma weight residual -180.00 -135.96 -44.04 0 5.00e+00 4.00e-02 7.76e+01 dihedral pdb=" CA VAL P 715 " pdb=" C VAL P 715 " pdb=" N PRO P 716 " pdb=" CA PRO P 716 " ideal model delta harmonic sigma weight residual 180.00 138.45 41.55 0 5.00e+00 4.00e-02 6.90e+01 ... (remaining 7500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1652 0.090 - 0.181: 191 0.181 - 0.271: 11 0.271 - 0.362: 4 0.362 - 0.452: 4 Chirality restraints: 1862 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 418 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 418 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 397 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1859 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 715 " 0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO M 716 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO M 716 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 716 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL P 715 " -0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO P 716 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO P 716 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO P 716 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 715 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C VAL P 715 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL P 715 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO P 716 " -0.015 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 1 2.01 - 2.73: 871 2.73 - 3.46: 16598 3.46 - 4.18: 28856 4.18 - 4.90: 47535 Nonbonded interactions: 93861 Sorted by model distance: nonbonded pdb=" N THR A 560 " pdb=" OG1 THR A 590 " model vdw 1.288 2.520 nonbonded pdb=" N TRP A 559 " pdb=" O ASP A 591 " model vdw 2.146 2.520 nonbonded pdb=" CA THR A 560 " pdb=" OG1 THR A 590 " model vdw 2.249 3.470 nonbonded pdb=" O THR A 593 " pdb=" ND2 ASN A 787 " model vdw 2.283 2.520 nonbonded pdb=" O SER A 323 " pdb=" OG SER A 326 " model vdw 2.288 2.440 ... (remaining 93856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'M' selection = chain 'P' } 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: 1.160 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: 0.010 Extract box with map and model: 5.560 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 34.640 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.006 0.066 11986 Z= 0.388 Angle : 1.020 10.352 16234 Z= 0.544 Chirality : 0.060 0.452 1862 Planarity : 0.007 0.098 2050 Dihedral : 9.959 77.545 4754 Min Nonbonded Distance : 1.288 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.81 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.68 % 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: -3.39 (0.20), residues: 1372 helix: -2.41 (0.29), residues: 180 sheet: -0.68 (0.35), residues: 200 loop : -2.78 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 251 HIS 0.014 0.003 HIS A 429 PHE 0.040 0.004 PHE P 714 TYR 0.026 0.003 TYR N 19 ARG 0.008 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.491 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 outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2975 time to fit residues: 70.5523 Evaluate side-chains 86 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 410 GLN A 417 HIS A 589 GLN A 610 GLN A 784 GLN ** B 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 187 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN L 4 GLN O 10 HIS P 711 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11986 Z= 0.284 Angle : 0.762 10.366 16234 Z= 0.382 Chirality : 0.047 0.255 1862 Planarity : 0.006 0.110 2050 Dihedral : 8.660 58.751 1990 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1372 helix: -1.82 (0.31), residues: 200 sheet: -0.82 (0.33), residues: 220 loop : -2.37 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 414 HIS 0.008 0.002 HIS A 1 PHE 0.019 0.002 PHE P 714 TYR 0.032 0.002 TYR K 19 ARG 0.006 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.444 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 outliers start: 2 outliers final: 0 residues processed: 103 average time/residue: 0.2652 time to fit residues: 39.3348 Evaluate side-chains 82 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** B 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN P 710 HIS ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11986 Z= 0.320 Angle : 0.775 9.933 16234 Z= 0.384 Chirality : 0.046 0.262 1862 Planarity : 0.005 0.065 2050 Dihedral : 8.527 58.671 1990 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.22), residues: 1372 helix: -1.58 (0.33), residues: 200 sheet: -1.09 (0.33), residues: 220 loop : -2.26 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 551 HIS 0.007 0.002 HIS A 1 PHE 0.019 0.002 PHE P 714 TYR 0.021 0.002 TYR K 19 ARG 0.006 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.483 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 outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2827 time to fit residues: 37.3267 Evaluate side-chains 72 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11986 Z= 0.151 Angle : 0.641 11.063 16234 Z= 0.317 Chirality : 0.046 0.270 1862 Planarity : 0.005 0.072 2050 Dihedral : 8.207 57.892 1990 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.22), residues: 1372 helix: -1.23 (0.34), residues: 194 sheet: -0.94 (0.33), residues: 214 loop : -2.05 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 493 HIS 0.007 0.001 HIS M 710 PHE 0.015 0.001 PHE M 701 TYR 0.022 0.001 TYR N 19 ARG 0.011 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 99 average time/residue: 0.2637 time to fit residues: 38.1401 Evaluate side-chains 80 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1555 time to fit residues: 2.0814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11986 Z= 0.155 Angle : 0.634 10.042 16234 Z= 0.311 Chirality : 0.045 0.256 1862 Planarity : 0.004 0.056 2050 Dihedral : 7.519 55.659 1990 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 0.08 % Allowed : 1.41 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.22), residues: 1372 helix: -1.09 (0.36), residues: 188 sheet: -0.75 (0.33), residues: 217 loop : -1.98 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 414 HIS 0.007 0.001 HIS M 710 PHE 0.012 0.001 PHE P 714 TYR 0.019 0.001 TYR M 708 ARG 0.014 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.488 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 outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.2517 time to fit residues: 33.4279 Evaluate side-chains 75 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1490 time to fit residues: 2.1861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11986 Z= 0.213 Angle : 0.657 8.150 16234 Z= 0.325 Chirality : 0.045 0.246 1862 Planarity : 0.004 0.057 2050 Dihedral : 7.386 51.212 1990 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.22), residues: 1372 helix: -1.19 (0.35), residues: 194 sheet: -0.80 (0.33), residues: 220 loop : -1.93 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 414 HIS 0.020 0.001 HIS M 710 PHE 0.014 0.001 PHE B 506 TYR 0.019 0.001 TYR N 19 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2556 time to fit residues: 31.5780 Evaluate side-chains 70 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 75 optimal weight: 50.0000 chunk 134 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 711 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11986 Z= 0.340 Angle : 0.792 8.604 16234 Z= 0.394 Chirality : 0.047 0.244 1862 Planarity : 0.005 0.059 2050 Dihedral : 7.678 51.659 1990 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 28.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.22), residues: 1372 helix: -1.71 (0.33), residues: 194 sheet: -0.98 (0.32), residues: 225 loop : -2.05 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 414 HIS 0.014 0.002 HIS M 710 PHE 0.033 0.003 PHE A 96 TYR 0.026 0.002 TYR N 19 ARG 0.010 0.001 ARG P 702 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2339 time to fit residues: 27.2443 Evaluate side-chains 62 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN P 710 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11986 Z= 0.265 Angle : 0.709 8.587 16234 Z= 0.352 Chirality : 0.046 0.253 1862 Planarity : 0.005 0.068 2050 Dihedral : 7.582 49.924 1990 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.22), residues: 1372 helix: -1.51 (0.33), residues: 194 sheet: -0.99 (0.32), residues: 228 loop : -1.97 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 493 HIS 0.014 0.002 HIS M 710 PHE 0.064 0.002 PHE P 714 TYR 0.031 0.002 TYR N 19 ARG 0.009 0.001 ARG A 780 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2356 time to fit residues: 27.5873 Evaluate side-chains 62 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 90 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 431 ASN A 784 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11986 Z= 0.167 Angle : 0.662 10.587 16234 Z= 0.324 Chirality : 0.047 0.345 1862 Planarity : 0.004 0.060 2050 Dihedral : 7.314 47.054 1990 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.22), residues: 1372 helix: -1.34 (0.35), residues: 194 sheet: -0.98 (0.32), residues: 227 loop : -1.86 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 493 HIS 0.017 0.001 HIS M 710 PHE 0.046 0.002 PHE P 714 TYR 0.026 0.001 TYR N 19 ARG 0.007 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2392 time to fit residues: 31.1467 Evaluate side-chains 67 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 118 optimal weight: 0.0010 overall best weight: 2.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN L 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11986 Z= 0.213 Angle : 0.675 9.752 16234 Z= 0.332 Chirality : 0.046 0.279 1862 Planarity : 0.004 0.063 2050 Dihedral : 7.151 45.688 1990 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.22), residues: 1372 helix: -1.26 (0.35), residues: 194 sheet: -0.96 (0.32), residues: 224 loop : -1.86 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 615 HIS 0.016 0.001 HIS M 710 PHE 0.045 0.002 PHE P 714 TYR 0.033 0.002 TYR M 708 ARG 0.004 0.000 ARG L 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2335 time to fit residues: 28.5787 Evaluate side-chains 64 residues out of total 1286 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.021141 restraints weight = 137855.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.021855 restraints weight = 95757.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.022395 restraints weight = 73448.887| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11986 Z= 0.319 Angle : 0.774 10.266 16234 Z= 0.381 Chirality : 0.047 0.245 1862 Planarity : 0.005 0.061 2050 Dihedral : 7.505 45.558 1990 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.22), residues: 1372 helix: -1.68 (0.32), residues: 200 sheet: -1.06 (0.32), residues: 226 loop : -2.01 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 493 HIS 0.016 0.002 HIS M 710 PHE 0.048 0.002 PHE P 714 TYR 0.032 0.002 TYR N 19 ARG 0.010 0.001 ARG A 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.86 seconds wall clock time: 40 minutes 11.17 seconds (2411.17 seconds total)