Starting phenix.real_space_refine on Wed Feb 21 16:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dis_27441/02_2024/8dis_27441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dis_27441/02_2024/8dis_27441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dis_27441/02_2024/8dis_27441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dis_27441/02_2024/8dis_27441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dis_27441/02_2024/8dis_27441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dis_27441/02_2024/8dis_27441.pdb" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14192 atoms to isotropic. 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 81 5.16 5 C 10704 2.51 5 N 2838 2.21 5 O 3421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "e PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 355": "OE1" <-> "OE2" Residue "e TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 491": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L ASP 93": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17044 Number of models: 1 Model: "" Number of chains: 30 Chain: "D" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "d" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "e" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "f" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1306 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "D" 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: "E" 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: "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: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "d" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "e" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "f" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 9.41, per 1000 atoms: 0.55 Number of scatterers: 17044 At special positions: 0 Unit cell: (136.35, 125.55, 143.775, 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 81 16.00 O 3421 8.00 N 2838 7.00 C 10704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS d 488 " - pdb=" SG CYS d 492 " distance=2.03 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 320 " distance=2.03 Simple disulfide: pdb=" SG CYS e 488 " - pdb=" SG CYS e 492 " distance=2.03 Simple disulfide: pdb=" SG CYS F 72 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 107 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 320 " distance=2.03 Simple disulfide: pdb=" SG CYS f 488 " - pdb=" SG CYS f 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG D 601 " - " ASN D 28 " " NAG D 602 " - " ASN D 304 " " NAG E 601 " - " ASN E 28 " " NAG E 602 " - " ASN E 304 " " NAG F 601 " - " ASN F 28 " " NAG F 602 " - " ASN F 304 " " NAG I 1 " - " ASN D 40 " " NAG J 1 " - " ASN D 104 " " NAG K 1 " - " ASN d 498 " " NAG M 1 " - " ASN E 40 " " NAG N 1 " - " ASN E 104 " " NAG O 1 " - " ASN e 498 " " NAG P 1 " - " ASN F 40 " " NAG Q 1 " - " ASN F 104 " " NAG R 1 " - " ASN f 498 " Time building additional restraints: 6.86 Conformation dependent library (CDL) restraints added in 2.9 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 48 sheets defined 18.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.548A pdb=" N LEU D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.647A pdb=" N TRP D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'd' and resid 381 through 402 Processing helix chain 'd' and resid 418 through 471 removed outlier: 3.996A pdb=" N GLU d 449 " --> pdb=" O LEU d 445 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG d 450 " --> pdb=" O LEU d 446 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS d 455 " --> pdb=" O THR d 451 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP d 456 " --> pdb=" O LEU d 452 " (cutoff:3.500A) Processing helix chain 'd' and resid 489 through 497 Processing helix chain 'd' and resid 503 through 507 Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'E' and resid 114 through 123 removed outlier: 3.534A pdb=" N LEU E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.642A pdb=" N TRP E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 Processing helix chain 'e' and resid 381 through 402 removed outlier: 3.508A pdb=" N THR e 385 " --> pdb=" O ASP e 381 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 471 removed outlier: 4.019A pdb=" N GLU e 449 " --> pdb=" O LEU e 445 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG e 450 " --> pdb=" O LEU e 446 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS e 455 " --> pdb=" O THR e 451 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP e 456 " --> pdb=" O LEU e 452 " (cutoff:3.500A) Processing helix chain 'e' and resid 489 through 497 Processing helix chain 'e' and resid 503 through 507 Processing helix chain 'F' and resid 73 through 80 Processing helix chain 'F' and resid 114 through 123 removed outlier: 3.505A pdb=" N LEU F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.644A pdb=" N TRP F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'f' and resid 381 through 402 removed outlier: 3.553A pdb=" N THR f 385 " --> pdb=" O ASP f 381 " (cutoff:3.500A) Processing helix chain 'f' and resid 418 through 471 removed outlier: 4.012A pdb=" N GLU f 449 " --> pdb=" O LEU f 445 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG f 450 " --> pdb=" O LEU f 446 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS f 455 " --> pdb=" O THR f 451 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP f 456 " --> pdb=" O LEU f 452 " (cutoff:3.500A) Processing helix chain 'f' and resid 489 through 497 Processing helix chain 'f' and resid 503 through 507 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.726A pdb=" N ASN C 31 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 32 " --> pdb=" O ILE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.715A pdb=" N ASP C 83 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 84 " --> pdb=" O THR C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.744A pdb=" N ASN L 31 " --> pdb=" O ASN L 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'd' and resid 376 through 380 Processing sheet with id=AA2, first strand: chain 'D' and resid 31 through 33 removed outlier: 4.585A pdb=" N ASP D 31 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 61 removed outlier: 6.188A pdb=" N LEU D 58 " --> pdb=" O HIS D 290 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N CYS D 292 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.792A pdb=" N LEU D 67 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 96 " --> pdb=" O ILE D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER D 127 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU D 189 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU D 193 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER D 127 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU D 189 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 155 removed outlier: 7.703A pdb=" N ALA D 152 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N LYS D 158 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.326A pdb=" N CYS D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 376 through 380 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 33 removed outlier: 4.569A pdb=" N ASP E 31 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 46 through 48 Processing sheet with id=AB6, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.176A pdb=" N LEU E 58 " --> pdb=" O HIS E 290 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS E 292 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 68 removed outlier: 6.787A pdb=" N LEU E 67 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE E 96 " --> pdb=" O ILE E 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 132 removed outlier: 3.673A pdb=" N SER E 127 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR E 270 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU E 193 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 272 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU E 189 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU E 193 " --> pdb=" O PRO E 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 125 through 132 removed outlier: 3.673A pdb=" N SER E 127 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR E 270 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU E 193 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE E 272 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU E 189 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 150 through 155 removed outlier: 7.717A pdb=" N ALA E 152 " --> pdb=" O LYS E 158 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N LYS E 158 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 178 through 183 Processing sheet with id=AC4, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AC5, first strand: chain 'f' and resid 376 through 380 Processing sheet with id=AC6, first strand: chain 'F' and resid 31 through 33 removed outlier: 4.564A pdb=" N ASP F 31 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 46 through 48 Processing sheet with id=AC8, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'F' and resid 58 through 61 removed outlier: 6.186A pdb=" N LEU F 58 " --> pdb=" O HIS F 290 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N CYS F 292 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 67 through 68 removed outlier: 6.786A pdb=" N LEU F 67 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE F 96 " --> pdb=" O ILE F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER F 127 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR F 270 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU F 193 " --> pdb=" O TYR F 270 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU F 189 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU F 193 " --> pdb=" O PRO F 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 125 through 132 removed outlier: 3.682A pdb=" N SER F 127 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR F 270 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU F 193 " --> pdb=" O TYR F 270 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU F 189 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 150 through 155 removed outlier: 7.712A pdb=" N ALA F 152 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LYS F 158 " --> pdb=" O ALA F 152 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 178 through 183 Processing sheet with id=AD6, first strand: chain 'F' and resid 301 through 302 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.560A pdb=" N ALA H 92 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.578A pdb=" N ALA A 92 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.632A pdb=" N ALA B 92 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.268A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AE6, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.477A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.467A pdb=" N VAL G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 17 through 23 Processing sheet with id=AE9, first strand: chain 'G' and resid 46 through 49 removed outlier: 6.509A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.531A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AF3, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.479A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1731 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: 5.71 Time building geometry restraints manager: 7.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 3 1.13 - 1.30: 2809 1.30 - 1.47: 7193 1.47 - 1.65: 7260 1.65 - 1.82: 114 Bond restraints: 17379 Sorted by residual: bond pdb=" CG PRO E 89 " pdb=" CD PRO E 89 " ideal model delta sigma weight residual 1.503 1.040 0.463 3.40e-02 8.65e+02 1.86e+02 bond pdb=" CG PRO D 89 " pdb=" CD PRO D 89 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 1.492 0.955 0.537 5.00e-02 4.00e+02 1.15e+02 bond pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " ideal model delta sigma weight residual 1.503 1.183 0.320 3.40e-02 8.65e+02 8.86e+01 bond pdb=" N PRO E 89 " pdb=" CD PRO E 89 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 17374 not shown) Histogram of bond angle deviations from ideal: 76.57 - 95.58: 8 95.58 - 114.58: 10700 114.58 - 133.58: 12839 133.58 - 152.59: 47 152.59 - 171.59: 1 Bond angle restraints: 23595 Sorted by residual: angle pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " ideal model delta sigma weight residual 106.10 171.59 -65.49 3.20e+00 9.77e-02 4.19e+02 angle pdb=" N PRO F 89 " pdb=" CD PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 103.20 78.74 24.46 1.50e+00 4.44e-01 2.66e+02 angle pdb=" N PRO E 89 " pdb=" CD PRO E 89 " pdb=" CG PRO E 89 " ideal model delta sigma weight residual 103.20 79.25 23.95 1.50e+00 4.44e-01 2.55e+02 angle pdb=" N PRO D 89 " pdb=" CD PRO D 89 " pdb=" CG PRO D 89 " ideal model delta sigma weight residual 103.20 79.33 23.87 1.50e+00 4.44e-01 2.53e+02 angle pdb=" CA PRO F 89 " pdb=" CB PRO F 89 " pdb=" CG PRO F 89 " ideal model delta sigma weight residual 104.50 76.57 27.93 1.90e+00 2.77e-01 2.16e+02 ... (remaining 23590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 9508 22.02 - 44.04: 889 44.04 - 66.07: 187 66.07 - 88.09: 44 88.09 - 110.11: 13 Dihedral angle restraints: 10641 sinusoidal: 4488 harmonic: 6153 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 51.44 41.56 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" N PRO F 89 " pdb=" CG PRO F 89 " pdb=" CD PRO F 89 " pdb=" CB PRO F 89 " ideal model delta sinusoidal sigma weight residual 30.00 91.43 -61.43 1 1.50e+01 4.44e-03 2.23e+01 dihedral pdb=" CB CYS E 72 " pdb=" SG CYS E 72 " pdb=" SG CYS E 84 " pdb=" CB CYS E 84 " ideal model delta sinusoidal sigma weight residual -86.00 -118.73 32.73 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 10638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2141 0.058 - 0.115: 428 0.115 - 0.173: 63 0.173 - 0.230: 4 0.230 - 0.288: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 NAG D 602 " pdb=" ND2 ASN D 304 " pdb=" C2 NAG D 602 " pdb=" O5 NAG D 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2637 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 95 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO L 96 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 298 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO D 299 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 88 " 0.032 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO F 89 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 89 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 89 " 0.026 5.00e-02 4.00e+02 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2382 2.76 - 3.29: 14086 3.29 - 3.83: 26474 3.83 - 4.36: 32641 4.36 - 4.90: 58666 Nonbonded interactions: 134249 Sorted by model distance: nonbonded pdb=" N GLU G 84 " pdb=" OE1 GLU G 84 " model vdw 2.224 2.520 nonbonded pdb=" O THR F 146 " pdb=" OG1 THR F 146 " model vdw 2.269 2.440 nonbonded pdb=" O THR E 146 " pdb=" OG1 THR E 146 " model vdw 2.270 2.440 nonbonded pdb=" O THR D 146 " pdb=" OG1 THR D 146 " model vdw 2.271 2.440 nonbonded pdb=" O GLY d 356 " pdb=" O HOH d 701 " model vdw 2.282 2.440 ... (remaining 134244 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' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' } 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 individual isotropic 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: 10.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 36.830 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 46.830 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 0.537 17379 Z= 0.658 Angle : 0.906 65.492 23595 Z= 0.475 Chirality : 0.048 0.288 2640 Planarity : 0.005 0.051 3012 Dihedral : 17.843 110.109 6675 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.67 % Favored : 95.90 % Rotamer: Outliers : 5.04 % Allowed : 22.81 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2124 helix: 1.84 (0.29), residues: 369 sheet: -0.11 (0.21), residues: 597 loop : -2.30 (0.14), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 92 HIS 0.005 0.001 HIS F 25 PHE 0.016 0.002 PHE D 128 TYR 0.008 0.001 TYR f 501 ARG 0.002 0.000 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 231 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: C 108 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4906 (tp) outliers start: 91 outliers final: 82 residues processed: 319 average time/residue: 1.1291 time to fit residues: 406.4710 Evaluate side-chains 307 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 223 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 355 GLU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 355 GLU Chi-restraints excluded: chain f residue 362 ILE Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 27 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17379 Z= 0.422 Angle : 0.718 12.579 23595 Z= 0.373 Chirality : 0.051 0.225 2640 Planarity : 0.006 0.051 3012 Dihedral : 10.679 71.212 2978 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.52 % Favored : 95.06 % Rotamer: Outliers : 6.87 % Allowed : 20.38 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2124 helix: 1.57 (0.28), residues: 372 sheet: -0.03 (0.21), residues: 600 loop : -2.19 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 92 HIS 0.008 0.001 HIS D 25 PHE 0.020 0.003 PHE D 128 TYR 0.011 0.002 TYR d 501 ARG 0.003 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 243 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: D 78 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7745 (mm) REVERT: D 113 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8207 (mp) REVERT: D 137 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: E 137 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: F 68 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7129 (tp40) REVERT: F 113 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8590 (mp) REVERT: F 137 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: f 394 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8348 (t0) REVERT: B 82 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7976 (tt0) outliers start: 124 outliers final: 65 residues processed: 340 average time/residue: 1.2463 time to fit residues: 472.0196 Evaluate side-chains 316 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 241 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 128 PHE Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 362 ILE Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain f residue 394 ASN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain L residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 chunk 151 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN e 469 GLN f 469 GLN H 39 GLN L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17379 Z= 0.189 Angle : 0.551 7.072 23595 Z= 0.288 Chirality : 0.046 0.241 2640 Planarity : 0.005 0.045 3012 Dihedral : 8.405 59.872 2913 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.30 % Favored : 96.33 % Rotamer: Outliers : 4.98 % Allowed : 22.65 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2124 helix: 1.81 (0.28), residues: 372 sheet: 0.40 (0.22), residues: 594 loop : -1.96 (0.15), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 436 HIS 0.004 0.001 HIS E 25 PHE 0.014 0.001 PHE e 353 TYR 0.010 0.001 TYR e 368 ARG 0.001 0.000 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 249 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6702 (mtm110) REVERT: D 78 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7742 (mm) REVERT: E 166 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8074 (tt) REVERT: E 291 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: F 137 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: A 82 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: B 82 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7916 (tt0) outliers start: 90 outliers final: 44 residues processed: 314 average time/residue: 1.2765 time to fit residues: 446.1904 Evaluate side-chains 288 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 362 ILE Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain G residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 200 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 179 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN e 469 GLN F 300 GLN f 390 ASN f 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17379 Z= 0.182 Angle : 0.536 6.631 23595 Z= 0.281 Chirality : 0.045 0.227 2640 Planarity : 0.004 0.045 3012 Dihedral : 7.183 58.916 2897 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.53 % Favored : 96.14 % Rotamer: Outliers : 4.98 % Allowed : 22.81 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2124 helix: 1.94 (0.28), residues: 372 sheet: 0.62 (0.22), residues: 594 loop : -1.85 (0.15), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.005 0.001 HIS F 25 PHE 0.014 0.001 PHE D 128 TYR 0.009 0.001 TYR f 368 ARG 0.001 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 249 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6705 (mtm110) REVERT: D 68 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: D 78 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7780 (mm) REVERT: E 166 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8068 (tt) REVERT: E 291 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: F 137 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: H 82 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: A 82 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: B 82 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7928 (tt0) outliers start: 90 outliers final: 42 residues processed: 311 average time/residue: 1.3340 time to fit residues: 460.2570 Evaluate side-chains 294 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain G residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 0.0570 chunk 179 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN E 300 GLN e 390 ASN e 469 GLN F 224 ASN f 390 ASN f 469 GLN L 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17379 Z= 0.265 Angle : 0.589 6.432 23595 Z= 0.309 Chirality : 0.047 0.222 2640 Planarity : 0.005 0.045 3012 Dihedral : 7.128 58.974 2892 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.91 % Favored : 95.81 % Rotamer: Outliers : 5.59 % Allowed : 22.15 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2124 helix: 1.89 (0.28), residues: 372 sheet: 0.65 (0.22), residues: 597 loop : -1.86 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 436 HIS 0.006 0.001 HIS F 25 PHE 0.018 0.002 PHE E 128 TYR 0.009 0.001 TYR d 368 ARG 0.001 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 241 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6725 (mtm110) REVERT: D 68 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: D 78 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7786 (mm) REVERT: D 291 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: E 166 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8077 (tt) REVERT: E 291 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: F 39 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7765 (mmtt) REVERT: F 68 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: F 113 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8458 (mp) REVERT: F 137 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: H 82 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: H 106 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: B 82 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7955 (tt0) outliers start: 101 outliers final: 53 residues processed: 313 average time/residue: 1.2888 time to fit residues: 448.4077 Evaluate side-chains 302 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN e 469 GLN ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 GLN L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17379 Z= 0.447 Angle : 0.694 7.476 23595 Z= 0.362 Chirality : 0.051 0.219 2640 Planarity : 0.005 0.053 3012 Dihedral : 7.239 59.434 2892 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.80 % Favored : 94.92 % Rotamer: Outliers : 6.37 % Allowed : 21.76 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2124 helix: 1.70 (0.28), residues: 372 sheet: 0.61 (0.22), residues: 597 loop : -1.95 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 77 HIS 0.009 0.001 HIS E 25 PHE 0.022 0.003 PHE F 128 TYR 0.011 0.002 TYR L 99 ARG 0.002 0.000 ARG F 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 239 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6777 (mtm110) REVERT: D 68 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: D 78 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7788 (mm) REVERT: E 166 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8139 (tt) REVERT: E 291 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: F 22 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8721 (mm) REVERT: F 39 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7735 (mmtt) REVERT: F 68 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7054 (tp40) REVERT: F 113 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8509 (mp) REVERT: F 137 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: F 291 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: f 382 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: H 82 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: H 106 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7095 (pm20) REVERT: B 82 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7997 (tt0) outliers start: 115 outliers final: 62 residues processed: 328 average time/residue: 1.2957 time to fit residues: 478.2578 Evaluate side-chains 316 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 239 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 382 GLN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 0.0870 chunk 124 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN f 469 GLN L 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17379 Z= 0.155 Angle : 0.520 6.350 23595 Z= 0.275 Chirality : 0.045 0.231 2640 Planarity : 0.004 0.043 3012 Dihedral : 6.961 58.830 2892 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.97 % Favored : 96.75 % Rotamer: Outliers : 3.65 % Allowed : 24.36 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2124 helix: 1.95 (0.28), residues: 372 sheet: 0.78 (0.22), residues: 594 loop : -1.77 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP f 436 HIS 0.003 0.001 HIS E 25 PHE 0.012 0.001 PHE e 353 TYR 0.008 0.001 TYR d 368 ARG 0.002 0.000 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6738 (mtm110) REVERT: D 78 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7739 (mm) REVERT: D 291 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: E 166 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8063 (tt) REVERT: F 137 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: H 82 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: B 82 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7952 (tt0) outliers start: 66 outliers final: 37 residues processed: 291 average time/residue: 1.3407 time to fit residues: 432.8217 Evaluate side-chains 281 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 237 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 366 TYR Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain G residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN e 469 GLN f 469 GLN L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17379 Z= 0.298 Angle : 0.606 6.151 23595 Z= 0.317 Chirality : 0.048 0.213 2640 Planarity : 0.005 0.046 3012 Dihedral : 7.040 59.587 2892 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.77 % Favored : 95.95 % Rotamer: Outliers : 4.37 % Allowed : 23.70 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2124 helix: 1.92 (0.28), residues: 372 sheet: 0.76 (0.22), residues: 597 loop : -1.82 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 77 HIS 0.007 0.001 HIS F 25 PHE 0.019 0.002 PHE F 128 TYR 0.009 0.001 TYR L 99 ARG 0.002 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 239 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6746 (mtm110) REVERT: D 78 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7739 (mm) REVERT: D 291 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: E 166 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8096 (tt) REVERT: F 22 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8685 (mm) REVERT: F 137 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: H 82 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: H 106 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: B 82 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7981 (tt0) outliers start: 79 outliers final: 48 residues processed: 296 average time/residue: 1.2928 time to fit residues: 425.0429 Evaluate side-chains 294 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 237 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 145 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN e 469 GLN F 286 ASN f 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17379 Z= 0.193 Angle : 0.539 6.201 23595 Z= 0.283 Chirality : 0.045 0.220 2640 Planarity : 0.004 0.044 3012 Dihedral : 6.892 59.814 2892 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.30 % Favored : 96.42 % Rotamer: Outliers : 3.71 % Allowed : 24.36 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2124 helix: 2.00 (0.28), residues: 372 sheet: 0.83 (0.22), residues: 594 loop : -1.74 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.005 0.001 HIS F 25 PHE 0.014 0.001 PHE D 128 TYR 0.009 0.001 TYR f 368 ARG 0.001 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 236 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6745 (mtm110) REVERT: D 68 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: D 78 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7742 (mm) REVERT: D 291 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: E 166 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8078 (tt) REVERT: E 226 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7097 (ttt90) REVERT: F 137 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: H 82 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: B 82 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7955 (tt0) outliers start: 67 outliers final: 45 residues processed: 286 average time/residue: 1.3299 time to fit residues: 422.5571 Evaluate side-chains 290 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 GLN d 469 GLN E 300 GLN e 469 GLN F 224 ASN f 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17379 Z= 0.338 Angle : 0.631 6.373 23595 Z= 0.329 Chirality : 0.048 0.204 2640 Planarity : 0.005 0.049 3012 Dihedral : 7.040 59.910 2892 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.86 % Favored : 95.86 % Rotamer: Outliers : 3.49 % Allowed : 24.97 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2124 helix: 1.88 (0.28), residues: 372 sheet: 0.78 (0.22), residues: 597 loop : -1.81 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 77 HIS 0.007 0.001 HIS F 25 PHE 0.019 0.002 PHE F 128 TYR 0.010 0.002 TYR L 99 ARG 0.002 0.000 ARG F 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 239 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6759 (mtm110) REVERT: D 78 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7764 (mm) REVERT: D 291 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: E 166 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8113 (tt) REVERT: F 137 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: f 382 GLN cc_start: 0.8213 (mp10) cc_final: 0.7706 (mp10) REVERT: H 82 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: B 82 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7975 (tt0) outliers start: 63 outliers final: 46 residues processed: 287 average time/residue: 1.3521 time to fit residues: 429.6524 Evaluate side-chains 292 residues out of total 1833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 239 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain e residue 394 ASN Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 153 CYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 288 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 168 optimal weight: 0.0040 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 469 GLN f 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.088160 restraints weight = 18750.401| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.56 r_work: 0.2844 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17379 Z= 0.161 Angle : 0.522 6.170 23595 Z= 0.274 Chirality : 0.045 0.217 2640 Planarity : 0.004 0.042 3012 Dihedral : 6.810 58.519 2892 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.06 % Favored : 96.66 % Rotamer: Outliers : 3.10 % Allowed : 25.30 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2124 helix: 2.01 (0.28), residues: 372 sheet: 0.86 (0.22), residues: 594 loop : -1.70 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 436 HIS 0.004 0.001 HIS F 25 PHE 0.012 0.001 PHE e 353 TYR 0.008 0.001 TYR f 368 ARG 0.001 0.000 ARG F 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7598.08 seconds wall clock time: 135 minutes 50.20 seconds (8150.20 seconds total)