Starting phenix.real_space_refine on Fri Mar 15 05:59:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ce9_7462/03_2024/6ce9_7462.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ce9_7462/03_2024/6ce9_7462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ce9_7462/03_2024/6ce9_7462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ce9_7462/03_2024/6ce9_7462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ce9_7462/03_2024/6ce9_7462.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ce9_7462/03_2024/6ce9_7462.pdb" } resolution = 4.3 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= 0.060 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 92 5.16 5 C 6828 2.51 5 N 1806 2.21 5 O 2056 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 TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" 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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10782 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" 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: "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: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 253 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 9 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: 9 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: 9 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: 6 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: 9 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: 9 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: 9 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: 6 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: 6.35, per 1000 atoms: 0.59 Number of scatterers: 10782 At special positions: 0 Unit cell: (95.7, 150.7, 85.8, 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 92 16.00 O 2056 8.00 N 1806 7.00 C 6828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, 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=2.03 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 B 8 " - pdb=" SG CYS B 26 " distance=2.02 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=2.02 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=2.03 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: 4.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 24 sheets defined 19.4% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.252A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.542A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.514A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.587A 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 255 through 264 removed outlier: 3.758A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.939A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.544A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.252A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.541A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.513A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 143 " --> pdb=" O VAL B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 143' Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.757A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 3.958A 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 356 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.939A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.543A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.905A pdb=" N LEU M 696 " --> pdb=" O ILE M 692 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER M 700 " --> pdb=" O LEU M 696 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU M 709 " --> pdb=" O PHE M 705 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS M 710 " --> pdb=" O GLU M 706 " (cutoff:3.500A) removed outlier: 4.614A 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: 3.739A 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: 3.737A 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: 3.905A pdb=" N LEU P 696 " --> pdb=" O ILE P 692 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER P 700 " --> pdb=" O LEU P 696 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 709 " --> pdb=" O PHE P 705 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS P 710 " --> pdb=" O GLU P 706 " (cutoff:3.500A) removed outlier: 4.615A 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: 6.650A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 65 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (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: 4.736A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.150A 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 233 removed outlier: 3.566A 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: 3.661A pdb=" N ARG A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 6.230A 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 318 through 321 Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.584A pdb=" N ILE A 336 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.724A pdb=" N GLU A 471 " --> pdb=" O LYS A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AB4, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.650A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 65 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS B 144 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB6, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AB7, first strand: chain 'B' and resid 212 through 216 removed outlier: 4.735A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.566A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.661A pdb=" N ARG B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC2, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AC3, first strand: chain 'B' and resid 335 through 336 removed outlier: 3.585A pdb=" N ILE B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.724A pdb=" N GLU B 471 " --> pdb=" O LYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AC6, first strand: chain 'B' and resid 532 through 534 226 hydrogen bonds defined for protein. 588 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: 3.52 Time building geometry restraints manager: 5.20 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: 3437 1.34 - 1.47: 2720 1.47 - 1.59: 4755 1.59 - 1.71: 0 1.71 - 1.83: 110 Bond restraints: 11022 Sorted by residual: bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C1 NAG B1015 " pdb=" O5 NAG B1015 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" C1 NAG A1015 " pdb=" O5 NAG A1015 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 ... (remaining 11017 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.82: 222 105.82 - 112.90: 6048 112.90 - 119.98: 3768 119.98 - 127.05: 4742 127.05 - 134.13: 142 Bond angle restraints: 14922 Sorted by residual: angle pdb=" C HIS A 1 " pdb=" N LEU A 2 " pdb=" CA LEU A 2 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C HIS B 1 " pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" N ASP A 542 " pdb=" CA ASP A 542 " pdb=" C ASP A 542 " ideal model delta sigma weight residual 109.81 118.47 -8.66 2.21e+00 2.05e-01 1.54e+01 angle pdb=" N ASP B 542 " pdb=" CA ASP B 542 " pdb=" C ASP B 542 " ideal model delta sigma weight residual 109.81 118.46 -8.65 2.21e+00 2.05e-01 1.53e+01 angle pdb=" N ILE A 136 " pdb=" CA ILE A 136 " pdb=" C ILE A 136 " ideal model delta sigma weight residual 112.96 109.05 3.91 1.00e+00 1.00e+00 1.53e+01 ... (remaining 14917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6778 21.38 - 42.75: 219 42.75 - 64.13: 21 64.13 - 85.51: 22 85.51 - 106.88: 8 Dihedral angle restraints: 7048 sinusoidal: 3298 harmonic: 3750 Sorted by residual: 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 -129.36 -50.64 0 5.00e+00 4.00e-02 1.03e+02 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 -129.40 -50.60 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA VAL M 715 " pdb=" C VAL M 715 " pdb=" N PRO M 716 " pdb=" CA PRO M 716 " ideal model delta harmonic sigma weight residual 180.00 139.05 40.95 0 5.00e+00 4.00e-02 6.71e+01 ... (remaining 7045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1499 0.088 - 0.175: 208 0.175 - 0.263: 5 0.263 - 0.351: 4 0.351 - 0.439: 4 Chirality restraints: 1720 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 397 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+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 4.47e+00 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 -1.98 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 1717 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 715 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO P 716 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO P 716 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO P 716 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 715 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO M 716 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO M 716 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO M 716 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 715 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C VAL P 715 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL P 715 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO P 716 " -0.017 2.00e-02 2.50e+03 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3339 2.83 - 3.35: 9921 3.35 - 3.87: 18724 3.87 - 4.38: 20091 4.38 - 4.90: 33375 Nonbonded interactions: 85450 Sorted by model distance: nonbonded pdb=" O SER B 323 " pdb=" OG SER B 326 " model vdw 2.314 2.440 nonbonded pdb=" O SER A 323 " pdb=" OG SER A 326 " model vdw 2.314 2.440 nonbonded pdb=" O CYS K 7 " pdb=" ND1 HIS L 5 " model vdw 2.314 2.520 nonbonded pdb=" O PRO A 558 " pdb=" OG1 THR A 560 " model vdw 2.314 2.440 nonbonded pdb=" O PRO B 558 " pdb=" OG1 THR B 560 " model vdw 2.314 2.440 ... (remaining 85445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.320 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: 5.690 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.640 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 11022 Z= 0.508 Angle : 1.059 10.212 14922 Z= 0.550 Chirality : 0.061 0.439 1720 Planarity : 0.007 0.111 1876 Dihedral : 11.758 106.882 4534 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.60 % Favored : 87.08 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.66 % 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 (0.21), residues: 1254 helix: -2.50 (0.29), residues: 170 sheet: -0.51 (0.45), residues: 132 loop : -2.69 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 251 HIS 0.015 0.003 HIS A 199 PHE 0.046 0.004 PHE M 714 TYR 0.028 0.004 TYR N 19 ARG 0.007 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9351 (mt0) cc_final: 0.9116 (mt0) REVERT: A 109 LEU cc_start: 0.9720 (tp) cc_final: 0.9497 (tp) REVERT: A 120 GLU cc_start: 0.9301 (tt0) cc_final: 0.9051 (tp30) REVERT: A 294 MET cc_start: 0.8546 (ppp) cc_final: 0.8067 (ppp) REVERT: A 322 ASP cc_start: 0.9403 (p0) cc_final: 0.9087 (p0) REVERT: A 442 MET cc_start: 0.9688 (ttt) cc_final: 0.9083 (tpt) REVERT: A 479 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8029 (ttp80) REVERT: A 480 THR cc_start: 0.8542 (p) cc_final: 0.8252 (t) REVERT: A 485 ILE cc_start: 0.9686 (mt) cc_final: 0.9464 (mm) REVERT: A 486 LEU cc_start: 0.9637 (tp) cc_final: 0.8914 (mt) REVERT: A 487 LEU cc_start: 0.9776 (mt) cc_final: 0.9453 (mm) REVERT: A 551 TRP cc_start: 0.9413 (t-100) cc_final: 0.8728 (t-100) REVERT: B 109 LEU cc_start: 0.9701 (tp) cc_final: 0.9386 (tp) REVERT: B 110 MET cc_start: 0.8619 (mmt) cc_final: 0.8336 (mmm) REVERT: B 178 PHE cc_start: 0.8918 (m-10) cc_final: 0.8592 (p90) REVERT: B 294 MET cc_start: 0.8709 (ppp) cc_final: 0.8201 (ppp) REVERT: B 322 ASP cc_start: 0.9462 (p0) cc_final: 0.9047 (p0) REVERT: B 376 LEU cc_start: 0.9377 (mt) cc_final: 0.9173 (tp) REVERT: B 442 MET cc_start: 0.9712 (ttt) cc_final: 0.9087 (tpt) REVERT: B 479 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8164 (ttp80) REVERT: B 486 LEU cc_start: 0.9658 (tp) cc_final: 0.9076 (mt) REVERT: B 487 LEU cc_start: 0.9722 (mt) cc_final: 0.9341 (mm) REVERT: L 11 LEU cc_start: 0.9625 (tp) cc_final: 0.9327 (tp) REVERT: L 18 VAL cc_start: 0.9290 (t) cc_final: 0.9038 (p) REVERT: P 697 GLU cc_start: 0.9193 (tt0) cc_final: 0.8752 (pt0) REVERT: P 707 ASP cc_start: 0.9202 (t70) cc_final: 0.8512 (t70) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2753 time to fit residues: 68.7970 Evaluate side-chains 101 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS ** A 108 ASN ** 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 328 GLN A 410 GLN A 417 HIS B 1 HIS ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN B 410 GLN B 417 HIS ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN O 10 HIS ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11022 Z= 0.212 Angle : 0.729 6.520 14922 Z= 0.370 Chirality : 0.048 0.256 1720 Planarity : 0.005 0.071 1876 Dihedral : 10.031 65.315 2000 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.50 % 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: -2.83 (0.23), residues: 1254 helix: -1.36 (0.33), residues: 194 sheet: -0.70 (0.36), residues: 178 loop : -2.44 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 551 HIS 0.004 0.001 HIS A 199 PHE 0.020 0.002 PHE P 714 TYR 0.027 0.002 TYR K 19 ARG 0.004 0.000 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.385 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: A 34 GLN cc_start: 0.9342 (mt0) cc_final: 0.9032 (mt0) REVERT: A 81 VAL cc_start: 0.9648 (t) cc_final: 0.9234 (t) REVERT: A 98 MET cc_start: 0.8846 (tpp) cc_final: 0.7648 (mmt) REVERT: A 101 LEU cc_start: 0.9791 (tp) cc_final: 0.9549 (mt) REVERT: A 120 GLU cc_start: 0.9333 (tt0) cc_final: 0.8944 (tt0) REVERT: A 294 MET cc_start: 0.8641 (ppp) cc_final: 0.8077 (ppp) REVERT: A 322 ASP cc_start: 0.9410 (p0) cc_final: 0.9023 (p0) REVERT: A 442 MET cc_start: 0.9658 (ttt) cc_final: 0.9047 (tpt) REVERT: A 551 TRP cc_start: 0.9340 (t-100) cc_final: 0.8853 (t-100) REVERT: B 34 GLN cc_start: 0.9546 (mt0) cc_final: 0.9323 (mt0) REVERT: B 54 LEU cc_start: 0.9382 (tp) cc_final: 0.9152 (tp) REVERT: B 294 MET cc_start: 0.8613 (ppp) cc_final: 0.7989 (ppp) REVERT: B 322 ASP cc_start: 0.9435 (p0) cc_final: 0.8968 (p0) REVERT: B 442 MET cc_start: 0.9659 (ttt) cc_final: 0.9176 (tpt) REVERT: B 485 ILE cc_start: 0.9813 (mm) cc_final: 0.9343 (mm) REVERT: B 486 LEU cc_start: 0.9733 (tp) cc_final: 0.9387 (tp) REVERT: M 703 LYS cc_start: 0.9401 (tptm) cc_final: 0.9132 (tptm) REVERT: M 706 GLU cc_start: 0.9213 (tp30) cc_final: 0.8943 (tp30) REVERT: P 697 GLU cc_start: 0.9154 (tt0) cc_final: 0.8913 (pt0) REVERT: P 706 GLU cc_start: 0.9309 (tp30) cc_final: 0.8732 (tp30) REVERT: P 720 ARG cc_start: 0.6365 (mmp80) cc_final: 0.3984 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2324 time to fit residues: 45.8624 Evaluate side-chains 92 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 0.0010 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 0.0030 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 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 431 ASN ** 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 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** L 10 HIS ** P 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11022 Z= 0.191 Angle : 0.680 7.672 14922 Z= 0.342 Chirality : 0.047 0.243 1720 Planarity : 0.005 0.061 1876 Dihedral : 8.464 61.838 2000 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -2.43 (0.24), residues: 1254 helix: -0.95 (0.35), residues: 178 sheet: -0.61 (0.36), residues: 176 loop : -2.12 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 559 HIS 0.004 0.001 HIS L 10 PHE 0.019 0.002 PHE P 714 TYR 0.024 0.001 TYR K 19 ARG 0.006 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9316 (mt0) cc_final: 0.9044 (mt0) REVERT: A 294 MET cc_start: 0.8422 (ppp) cc_final: 0.7774 (ppp) REVERT: A 322 ASP cc_start: 0.9348 (p0) cc_final: 0.8951 (p0) REVERT: A 442 MET cc_start: 0.9628 (ttt) cc_final: 0.9045 (tpt) REVERT: A 551 TRP cc_start: 0.9309 (t-100) cc_final: 0.8889 (t-100) REVERT: A 553 MET cc_start: 0.9202 (tpt) cc_final: 0.8990 (tpp) REVERT: B 34 GLN cc_start: 0.9499 (mt0) cc_final: 0.9217 (mt0) REVERT: B 54 LEU cc_start: 0.9423 (tp) cc_final: 0.9208 (tp) REVERT: B 294 MET cc_start: 0.8587 (ppp) cc_final: 0.7991 (ppp) REVERT: B 322 ASP cc_start: 0.9430 (p0) cc_final: 0.8935 (p0) REVERT: B 442 MET cc_start: 0.9648 (ttt) cc_final: 0.9138 (tmm) REVERT: B 485 ILE cc_start: 0.9824 (mm) cc_final: 0.9383 (mm) REVERT: B 486 LEU cc_start: 0.9662 (tp) cc_final: 0.9331 (tp) REVERT: B 504 MET cc_start: 0.9189 (mmp) cc_final: 0.8920 (mmp) REVERT: M 703 LYS cc_start: 0.9370 (tptm) cc_final: 0.9048 (tptm) REVERT: M 706 GLU cc_start: 0.9310 (tp30) cc_final: 0.8833 (tp30) REVERT: O 9 SER cc_start: 0.9121 (m) cc_final: 0.8563 (m) REVERT: O 13 GLU cc_start: 0.9632 (mm-30) cc_final: 0.9325 (mm-30) REVERT: P 697 GLU cc_start: 0.9124 (tt0) cc_final: 0.8261 (pp20) REVERT: P 706 GLU cc_start: 0.9474 (tp30) cc_final: 0.9149 (tp30) REVERT: P 720 ARG cc_start: 0.6595 (mmp80) cc_final: 0.3989 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2318 time to fit residues: 39.5055 Evaluate side-chains 90 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11022 Z= 0.311 Angle : 0.751 9.654 14922 Z= 0.370 Chirality : 0.046 0.233 1720 Planarity : 0.005 0.061 1876 Dihedral : 7.931 61.633 2000 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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 (0.24), residues: 1254 helix: -1.17 (0.35), residues: 178 sheet: -0.54 (0.37), residues: 176 loop : -1.98 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.004 0.001 HIS B 100 PHE 0.015 0.002 PHE P 714 TYR 0.025 0.002 TYR N 19 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9117 (mt0) cc_final: 0.8855 (mt0) REVERT: A 81 VAL cc_start: 0.9659 (t) cc_final: 0.9182 (t) REVERT: A 98 MET cc_start: 0.8443 (mmp) cc_final: 0.8165 (mmm) REVERT: A 294 MET cc_start: 0.8280 (ppp) cc_final: 0.7646 (ppp) REVERT: A 322 ASP cc_start: 0.9372 (p0) cc_final: 0.8990 (p0) REVERT: A 442 MET cc_start: 0.9658 (ttt) cc_final: 0.9191 (tmm) REVERT: A 479 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7938 (ttp80) REVERT: A 486 LEU cc_start: 0.9729 (tp) cc_final: 0.9070 (mt) REVERT: A 551 TRP cc_start: 0.9329 (t-100) cc_final: 0.8862 (t-100) REVERT: B 34 GLN cc_start: 0.9343 (mt0) cc_final: 0.9049 (mt0) REVERT: B 294 MET cc_start: 0.8615 (ppp) cc_final: 0.8080 (ppp) REVERT: B 322 ASP cc_start: 0.9421 (p0) cc_final: 0.9039 (p0) REVERT: B 442 MET cc_start: 0.9678 (ttt) cc_final: 0.9236 (tmm) REVERT: B 486 LEU cc_start: 0.9702 (tp) cc_final: 0.9078 (tp) REVERT: M 703 LYS cc_start: 0.9416 (tptm) cc_final: 0.9094 (tptm) REVERT: M 706 GLU cc_start: 0.9278 (tp30) cc_final: 0.8764 (tp30) REVERT: L 13 GLU cc_start: 0.9141 (mp0) cc_final: 0.8924 (mp0) REVERT: O 13 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9313 (mm-30) REVERT: P 697 GLU cc_start: 0.9096 (tt0) cc_final: 0.8256 (pp20) REVERT: P 706 GLU cc_start: 0.9512 (tp30) cc_final: 0.9107 (tp30) REVERT: P 720 ARG cc_start: 0.7056 (mmp80) cc_final: 0.4489 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2270 time to fit residues: 35.7100 Evaluate side-chains 82 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 51 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 431 ASN ** 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 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** P 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11022 Z= 0.246 Angle : 0.688 6.727 14922 Z= 0.343 Chirality : 0.046 0.238 1720 Planarity : 0.005 0.062 1876 Dihedral : 7.552 59.159 2000 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.27 (0.24), residues: 1254 helix: -1.08 (0.36), residues: 178 sheet: -0.51 (0.36), residues: 176 loop : -1.94 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.004 0.001 HIS A 32 PHE 0.057 0.002 PHE P 714 TYR 0.032 0.002 TYR N 19 ARG 0.010 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 VAL cc_start: 0.9656 (t) cc_final: 0.9174 (t) REVERT: A 98 MET cc_start: 0.8047 (mmp) cc_final: 0.7634 (mmm) REVERT: A 101 LEU cc_start: 0.9669 (mt) cc_final: 0.9289 (mt) REVERT: A 294 MET cc_start: 0.8335 (ppp) cc_final: 0.7724 (ppp) REVERT: A 322 ASP cc_start: 0.9276 (p0) cc_final: 0.8882 (p0) REVERT: A 442 MET cc_start: 0.9628 (ttt) cc_final: 0.9162 (tmm) REVERT: A 473 LEU cc_start: 0.9007 (mt) cc_final: 0.8801 (mt) REVERT: A 479 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7885 (ttp80) REVERT: A 486 LEU cc_start: 0.9725 (tp) cc_final: 0.9047 (mt) REVERT: A 504 MET cc_start: 0.9164 (mmm) cc_final: 0.8915 (mmm) REVERT: A 551 TRP cc_start: 0.9362 (t-100) cc_final: 0.8855 (t-100) REVERT: A 553 MET cc_start: 0.9238 (tpt) cc_final: 0.9035 (tpp) REVERT: B 34 GLN cc_start: 0.9348 (mt0) cc_final: 0.9002 (mt0) REVERT: B 54 LEU cc_start: 0.9518 (tp) cc_final: 0.9303 (tp) REVERT: B 81 VAL cc_start: 0.9652 (t) cc_final: 0.9448 (t) REVERT: B 98 MET cc_start: 0.8977 (mmm) cc_final: 0.8545 (mmm) REVERT: B 101 LEU cc_start: 0.9731 (mt) cc_final: 0.9272 (mt) REVERT: B 294 MET cc_start: 0.8553 (ppp) cc_final: 0.7945 (ppp) REVERT: B 442 MET cc_start: 0.9651 (ttt) cc_final: 0.9237 (tmm) REVERT: B 443 GLU cc_start: 0.9492 (OUTLIER) cc_final: 0.9233 (pm20) REVERT: B 486 LEU cc_start: 0.9624 (tp) cc_final: 0.9329 (tp) REVERT: B 504 MET cc_start: 0.9372 (mmp) cc_final: 0.9059 (mmm) REVERT: M 703 LYS cc_start: 0.9411 (tptm) cc_final: 0.9075 (tptm) REVERT: M 706 GLU cc_start: 0.9280 (tp30) cc_final: 0.8720 (tp30) REVERT: O 13 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9319 (mm-30) REVERT: P 697 GLU cc_start: 0.9090 (tt0) cc_final: 0.8380 (pp20) REVERT: P 706 GLU cc_start: 0.9493 (tp30) cc_final: 0.9109 (tp30) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2126 time to fit residues: 33.3023 Evaluate side-chains 77 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 24 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.5922 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** 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 431 ASN ** 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 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** P 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11022 Z= 0.192 Angle : 0.677 11.548 14922 Z= 0.334 Chirality : 0.046 0.238 1720 Planarity : 0.004 0.056 1876 Dihedral : 7.929 61.593 2000 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.16 (0.24), residues: 1254 helix: -0.93 (0.37), residues: 176 sheet: -0.43 (0.36), residues: 178 loop : -1.88 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 559 HIS 0.003 0.001 HIS L 5 PHE 0.054 0.002 PHE M 714 TYR 0.027 0.001 TYR N 19 ARG 0.007 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9456 (mt0) cc_final: 0.9230 (mt0) REVERT: A 81 VAL cc_start: 0.9636 (t) cc_final: 0.9179 (t) REVERT: A 322 ASP cc_start: 0.9216 (p0) cc_final: 0.8818 (p0) REVERT: A 442 MET cc_start: 0.9609 (ttt) cc_final: 0.9196 (tmm) REVERT: A 473 LEU cc_start: 0.9001 (mt) cc_final: 0.8784 (mt) REVERT: A 479 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7848 (ttp80) REVERT: A 486 LEU cc_start: 0.9708 (tp) cc_final: 0.9026 (mt) REVERT: A 504 MET cc_start: 0.9159 (mmm) cc_final: 0.8888 (mmm) REVERT: A 551 TRP cc_start: 0.9344 (t-100) cc_final: 0.8858 (t-100) REVERT: A 553 MET cc_start: 0.9194 (tpt) cc_final: 0.8989 (tpp) REVERT: B 34 GLN cc_start: 0.9333 (mt0) cc_final: 0.9056 (mt0) REVERT: B 54 LEU cc_start: 0.9536 (tp) cc_final: 0.9318 (tp) REVERT: B 81 VAL cc_start: 0.9649 (t) cc_final: 0.9443 (t) REVERT: B 442 MET cc_start: 0.9635 (ttt) cc_final: 0.9223 (tmm) REVERT: B 473 LEU cc_start: 0.9006 (mt) cc_final: 0.8796 (mt) REVERT: B 486 LEU cc_start: 0.9624 (tp) cc_final: 0.9356 (tp) REVERT: B 504 MET cc_start: 0.9368 (mmp) cc_final: 0.9067 (mmm) REVERT: M 706 GLU cc_start: 0.9246 (tp30) cc_final: 0.8689 (tp30) REVERT: L 13 GLU cc_start: 0.9216 (mp0) cc_final: 0.8968 (mp0) REVERT: O 9 SER cc_start: 0.9178 (m) cc_final: 0.8694 (m) REVERT: O 13 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9351 (mm-30) REVERT: P 697 GLU cc_start: 0.9103 (tt0) cc_final: 0.8438 (pp20) REVERT: P 706 GLU cc_start: 0.9497 (tp30) cc_final: 0.9042 (tp30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2213 time to fit residues: 33.2859 Evaluate side-chains 80 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 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 431 ASN ** 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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11022 Z= 0.225 Angle : 0.689 11.682 14922 Z= 0.337 Chirality : 0.046 0.234 1720 Planarity : 0.005 0.057 1876 Dihedral : 7.865 67.905 2000 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.12 (0.24), residues: 1254 helix: -0.96 (0.37), residues: 176 sheet: -0.32 (0.36), residues: 176 loop : -1.86 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 559 HIS 0.004 0.001 HIS B 100 PHE 0.041 0.002 PHE M 714 TYR 0.026 0.002 TYR N 19 ARG 0.005 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9409 (mt0) cc_final: 0.9178 (mt0) REVERT: A 81 VAL cc_start: 0.9638 (t) cc_final: 0.9167 (t) REVERT: A 322 ASP cc_start: 0.9256 (p0) cc_final: 0.8878 (p0) REVERT: A 442 MET cc_start: 0.9620 (ttt) cc_final: 0.9232 (tmm) REVERT: A 473 LEU cc_start: 0.8973 (mt) cc_final: 0.8756 (mt) REVERT: A 479 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7760 (ttp80) REVERT: A 486 LEU cc_start: 0.9737 (tp) cc_final: 0.9088 (mt) REVERT: A 504 MET cc_start: 0.9137 (mmm) cc_final: 0.8868 (mmm) REVERT: A 553 MET cc_start: 0.9226 (tpt) cc_final: 0.8978 (tpp) REVERT: A 554 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7299 (mtm-85) REVERT: B 54 LEU cc_start: 0.9549 (tp) cc_final: 0.9343 (tp) REVERT: B 81 VAL cc_start: 0.9673 (t) cc_final: 0.9457 (t) REVERT: B 442 MET cc_start: 0.9624 (ttt) cc_final: 0.9230 (tmm) REVERT: B 473 LEU cc_start: 0.9012 (mt) cc_final: 0.8808 (mt) REVERT: B 486 LEU cc_start: 0.9629 (tp) cc_final: 0.9370 (tp) REVERT: B 504 MET cc_start: 0.9360 (mmp) cc_final: 0.9058 (mmm) REVERT: M 703 LYS cc_start: 0.9456 (tptm) cc_final: 0.9142 (tptm) REVERT: M 706 GLU cc_start: 0.9240 (tp30) cc_final: 0.8689 (tp30) REVERT: L 13 GLU cc_start: 0.9222 (mp0) cc_final: 0.9006 (mp0) REVERT: O 13 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9369 (mm-30) REVERT: P 697 GLU cc_start: 0.9144 (tt0) cc_final: 0.8472 (pp20) REVERT: P 706 GLU cc_start: 0.9489 (tp30) cc_final: 0.9033 (tp30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2231 time to fit residues: 31.5301 Evaluate side-chains 73 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 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 407 ASN ** A 431 ASN ** 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 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** P 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11022 Z= 0.308 Angle : 0.745 11.263 14922 Z= 0.364 Chirality : 0.046 0.234 1720 Planarity : 0.005 0.057 1876 Dihedral : 7.712 58.095 2000 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.38 (0.23), residues: 1254 helix: -1.17 (0.35), residues: 176 sheet: -0.56 (0.34), residues: 196 loop : -2.06 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 559 HIS 0.004 0.001 HIS A 100 PHE 0.038 0.002 PHE M 714 TYR 0.027 0.002 TYR N 19 ARG 0.005 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9423 (mt0) cc_final: 0.9179 (mt0) REVERT: A 81 VAL cc_start: 0.9675 (t) cc_final: 0.9245 (t) REVERT: A 442 MET cc_start: 0.9631 (ttt) cc_final: 0.9265 (tmm) REVERT: A 473 LEU cc_start: 0.9017 (mt) cc_final: 0.8798 (mt) REVERT: A 479 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7632 (ttp80) REVERT: A 486 LEU cc_start: 0.9753 (tp) cc_final: 0.9088 (mt) REVERT: A 504 MET cc_start: 0.9118 (mmm) cc_final: 0.8853 (mmm) REVERT: A 553 MET cc_start: 0.9250 (tpt) cc_final: 0.8987 (tpp) REVERT: A 554 ARG cc_start: 0.8083 (mtm180) cc_final: 0.7386 (mtm-85) REVERT: B 81 VAL cc_start: 0.9671 (t) cc_final: 0.9400 (t) REVERT: B 442 MET cc_start: 0.9634 (ttt) cc_final: 0.9243 (tmm) REVERT: B 486 LEU cc_start: 0.9645 (tp) cc_final: 0.9394 (tp) REVERT: B 504 MET cc_start: 0.9300 (mmp) cc_final: 0.9093 (mmm) REVERT: M 703 LYS cc_start: 0.9428 (tptm) cc_final: 0.9094 (tptm) REVERT: M 706 GLU cc_start: 0.9356 (tp30) cc_final: 0.8794 (tp30) REVERT: L 13 GLU cc_start: 0.9241 (mp0) cc_final: 0.9025 (mp0) REVERT: O 13 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9370 (mm-30) REVERT: O 26 TYR cc_start: 0.9058 (t80) cc_final: 0.8806 (t80) REVERT: P 697 GLU cc_start: 0.9129 (tt0) cc_final: 0.8498 (pp20) REVERT: P 706 GLU cc_start: 0.9501 (tp30) cc_final: 0.9014 (tp30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2236 time to fit residues: 29.2929 Evaluate side-chains 73 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 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** P 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11022 Z= 0.221 Angle : 0.685 10.843 14922 Z= 0.337 Chirality : 0.046 0.236 1720 Planarity : 0.004 0.057 1876 Dihedral : 7.184 52.713 2000 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.28 (0.23), residues: 1254 helix: -1.02 (0.36), residues: 176 sheet: -0.59 (0.34), residues: 196 loop : -1.97 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 493 HIS 0.007 0.001 HIS B 440 PHE 0.032 0.002 PHE M 714 TYR 0.026 0.002 TYR N 19 ARG 0.004 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9408 (mt0) cc_final: 0.9152 (mt0) REVERT: A 81 VAL cc_start: 0.9647 (t) cc_final: 0.9205 (t) REVERT: A 98 MET cc_start: 0.8363 (mmm) cc_final: 0.7445 (mmm) REVERT: A 442 MET cc_start: 0.9604 (ttt) cc_final: 0.9188 (tmm) REVERT: A 473 LEU cc_start: 0.9000 (mt) cc_final: 0.8777 (mt) REVERT: A 479 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7537 (ttp80) REVERT: A 486 LEU cc_start: 0.9714 (tp) cc_final: 0.9047 (mt) REVERT: A 504 MET cc_start: 0.9086 (mmm) cc_final: 0.8827 (mmm) REVERT: A 553 MET cc_start: 0.9198 (tpt) cc_final: 0.8951 (tpp) REVERT: A 554 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7473 (mtm-85) REVERT: B 81 VAL cc_start: 0.9668 (t) cc_final: 0.9392 (t) REVERT: B 442 MET cc_start: 0.9625 (ttt) cc_final: 0.9254 (tmm) REVERT: B 473 LEU cc_start: 0.9042 (mt) cc_final: 0.8824 (mt) REVERT: B 486 LEU cc_start: 0.9613 (tp) cc_final: 0.9382 (tp) REVERT: B 504 MET cc_start: 0.9313 (mmp) cc_final: 0.9091 (mmm) REVERT: M 703 LYS cc_start: 0.9407 (tptm) cc_final: 0.9042 (tptm) REVERT: M 706 GLU cc_start: 0.9394 (tp30) cc_final: 0.9031 (tp30) REVERT: L 13 GLU cc_start: 0.9191 (mp0) cc_final: 0.8976 (mp0) REVERT: O 13 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9369 (mm-30) REVERT: O 26 TYR cc_start: 0.8999 (t80) cc_final: 0.8763 (t80) REVERT: P 697 GLU cc_start: 0.9126 (tt0) cc_final: 0.8533 (pp20) REVERT: P 706 GLU cc_start: 0.9470 (tp30) cc_final: 0.9035 (tp30) REVERT: P 707 ASP cc_start: 0.9197 (t70) cc_final: 0.8997 (t70) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2064 time to fit residues: 27.6242 Evaluate side-chains 75 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 127 optimal weight: 0.0040 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** 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 431 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11022 Z= 0.188 Angle : 0.661 9.047 14922 Z= 0.325 Chirality : 0.045 0.235 1720 Planarity : 0.004 0.053 1876 Dihedral : 6.774 49.866 2000 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.09 (0.24), residues: 1254 helix: -0.89 (0.36), residues: 176 sheet: -0.35 (0.36), residues: 176 loop : -1.84 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.004 0.001 HIS A 209 PHE 0.030 0.002 PHE M 714 TYR 0.024 0.002 TYR N 19 ARG 0.003 0.000 ARG B 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.9406 (mt0) cc_final: 0.9140 (mt0) REVERT: A 81 VAL cc_start: 0.9643 (t) cc_final: 0.9225 (t) REVERT: A 87 LEU cc_start: 0.9362 (mt) cc_final: 0.8977 (tp) REVERT: A 98 MET cc_start: 0.8470 (mmm) cc_final: 0.7582 (mmm) REVERT: A 109 LEU cc_start: 0.9729 (tp) cc_final: 0.9478 (tp) REVERT: A 120 GLU cc_start: 0.9151 (tt0) cc_final: 0.8759 (tt0) REVERT: A 442 MET cc_start: 0.9599 (ttt) cc_final: 0.9170 (tmm) REVERT: A 473 LEU cc_start: 0.9006 (mt) cc_final: 0.8776 (mt) REVERT: A 479 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7475 (ttp80) REVERT: A 486 LEU cc_start: 0.9700 (tp) cc_final: 0.9049 (mt) REVERT: A 504 MET cc_start: 0.9083 (mmm) cc_final: 0.8829 (mmm) REVERT: A 553 MET cc_start: 0.9231 (tpt) cc_final: 0.8964 (tpp) REVERT: A 554 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7385 (mtm-85) REVERT: B 81 VAL cc_start: 0.9669 (t) cc_final: 0.9400 (t) REVERT: B 87 LEU cc_start: 0.9291 (mt) cc_final: 0.8949 (tp) REVERT: B 442 MET cc_start: 0.9597 (ttt) cc_final: 0.9217 (tmm) REVERT: B 473 LEU cc_start: 0.9053 (mt) cc_final: 0.8834 (mt) REVERT: B 486 LEU cc_start: 0.9624 (tp) cc_final: 0.9407 (tp) REVERT: M 703 LYS cc_start: 0.9399 (tptm) cc_final: 0.9023 (tptm) REVERT: M 706 GLU cc_start: 0.9388 (tp30) cc_final: 0.9015 (tp30) REVERT: L 13 GLU cc_start: 0.9185 (mp0) cc_final: 0.8938 (mp0) REVERT: O 13 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9372 (mm-30) REVERT: O 26 TYR cc_start: 0.8974 (t80) cc_final: 0.8771 (t80) REVERT: P 697 GLU cc_start: 0.9105 (tt0) cc_final: 0.8528 (pp20) REVERT: P 706 GLU cc_start: 0.9460 (tp30) cc_final: 0.9007 (tp30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2129 time to fit residues: 30.5809 Evaluate side-chains 82 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** 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 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.046034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.034674 restraints weight = 66341.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035882 restraints weight = 45231.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036804 restraints weight = 34263.690| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11022 Z= 0.200 Angle : 0.661 8.027 14922 Z= 0.327 Chirality : 0.046 0.254 1720 Planarity : 0.004 0.057 1876 Dihedral : 6.680 47.673 2000 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.05 (0.24), residues: 1254 helix: -0.86 (0.36), residues: 176 sheet: -0.21 (0.36), residues: 174 loop : -1.83 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 199 PHE 0.028 0.002 PHE M 714 TYR 0.024 0.002 TYR N 14 ARG 0.006 0.000 ARG A 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.13 seconds wall clock time: 37 minutes 42.92 seconds (2262.92 seconds total)