Starting phenix.real_space_refine on Sun Mar 17 08:33:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/03_2024/7sco_25040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/03_2024/7sco_25040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/03_2024/7sco_25040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/03_2024/7sco_25040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/03_2024/7sco_25040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/03_2024/7sco_25040.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10767 2.51 5 N 2916 2.21 5 O 3375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17130 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 900 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 900 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "F" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1382 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 900 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "K" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} 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: 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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.90, per 1000 atoms: 0.52 Number of scatterers: 17130 At special positions: 0 Unit cell: (129.95, 139.15, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3375 8.00 N 2916 7.00 C 10767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS H 529 " - pdb=" SG CYS H 603 " distance=2.02 Simple disulfide: pdb=" SG CYS L 644 " - pdb=" SG CYS L 710 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 603 " distance=2.02 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 710 " distance=2.02 Simple disulfide: pdb=" SG CYS G 8 " - pdb=" SG CYS I 467 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 278 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 71 " distance=2.02 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 282 " - pdb=" SG CYS G 306 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS J 529 " - pdb=" SG CYS J 603 " distance=2.02 Simple disulfide: pdb=" SG CYS K 644 " - pdb=" SG CYS K 710 " distance=2.02 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 15 " " NAG A 402 " - " ASN A 27 " " NAG A 403 " - " ASN A 58 " " NAG A 404 " - " ASN A 129 " " NAG C 401 " - " ASN C 15 " " NAG C 402 " - " ASN C 27 " " NAG C 403 " - " ASN C 58 " " NAG C 404 " - " ASN C 129 " " NAG G 401 " - " ASN G 15 " " NAG G 402 " - " ASN G 27 " " NAG G 403 " - " ASN G 58 " " NAG G 404 " - " ASN G 129 " " NAG M 1 " - " ASN A 91 " " NAG N 1 " - " ASN C 91 " " NAG O 1 " - " ASN G 91 " Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.0 seconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 23.4% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.869A pdb=" N GLU A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 73 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 removed outlier: 3.529A pdb=" N GLU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 388 Processing helix chain 'B' and resid 404 through 457 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 502 through 504 No H-bonds generated for 'chain 'B' and resid 502 through 504' Processing helix chain 'H' and resid 535 through 539 Processing helix chain 'H' and resid 569 through 572 Processing helix chain 'H' and resid 594 through 598 Processing helix chain 'L' and resid 701 through 705 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.869A pdb=" N GLU C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU C 73 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 removed outlier: 3.530A pdb=" N GLU C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 367 through 388 Processing helix chain 'D' and resid 404 through 457 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 488 through 491 Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 569 through 572 Processing helix chain 'E' and resid 594 through 598 Processing helix chain 'F' and resid 701 through 705 Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'G' and resid 60 through 67 Processing helix chain 'G' and resid 68 through 75 removed outlier: 3.870A pdb=" N GLU G 72 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.529A pdb=" N GLU G 107 " --> pdb=" O GLU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'I' and resid 367 through 388 Processing helix chain 'I' and resid 404 through 457 Processing helix chain 'I' and resid 475 through 485 Processing helix chain 'I' and resid 488 through 491 Processing helix chain 'I' and resid 492 through 501 Processing helix chain 'I' and resid 502 through 504 No H-bonds generated for 'chain 'I' and resid 502 through 504' Processing helix chain 'J' and resid 535 through 539 Processing helix chain 'J' and resid 569 through 572 Processing helix chain 'J' and resid 594 through 598 Processing helix chain 'K' and resid 701 through 705 Processing sheet with id=AA1, first strand: chain 'B' and resid 361 through 366 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.511A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.452A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 287 through 289 Processing sheet with id=AB2, first strand: chain 'H' and resid 510 through 513 Processing sheet with id=AB3, first strand: chain 'H' and resid 517 through 519 removed outlier: 6.002A pdb=" N ARG H 545 " --> pdb=" O TRP H 554 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP H 554 " --> pdb=" O ARG H 545 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET H 555 " --> pdb=" O TYR H 567 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR H 567 " --> pdb=" O MET H 555 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG H 557 " --> pdb=" O GLU H 565 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU H 565 " --> pdb=" O ARG H 557 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 517 through 519 Processing sheet with id=AB5, first strand: chain 'L' and resid 625 through 626 Processing sheet with id=AB6, first strand: chain 'L' and resid 632 through 634 removed outlier: 7.003A pdb=" N LEU L 632 " --> pdb=" O GLU L 727 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 657 " --> pdb=" O LEU L 669 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 361 through 366 Processing sheet with id=AB8, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AC2, first strand: chain 'C' and resid 54 through 57 removed outlier: 6.512A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 112 through 119 removed outlier: 6.747A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 112 through 119 removed outlier: 6.747A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.453A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'C' and resid 287 through 289 Processing sheet with id=AC8, first strand: chain 'E' and resid 510 through 513 Processing sheet with id=AC9, first strand: chain 'E' and resid 517 through 519 removed outlier: 6.002A pdb=" N ARG E 545 " --> pdb=" O TRP E 554 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP E 554 " --> pdb=" O ARG E 545 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET E 555 " --> pdb=" O TYR E 567 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR E 567 " --> pdb=" O MET E 555 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG E 557 " --> pdb=" O GLU E 565 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU E 565 " --> pdb=" O ARG E 557 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 517 through 519 Processing sheet with id=AD2, first strand: chain 'F' and resid 625 through 626 Processing sheet with id=AD3, first strand: chain 'F' and resid 632 through 634 removed outlier: 7.003A pdb=" N LEU F 632 " --> pdb=" O GLU F 727 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP F 657 " --> pdb=" O LEU F 669 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 361 through 366 Processing sheet with id=AD5, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD6, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AD7, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AD8, first strand: chain 'G' and resid 54 through 57 removed outlier: 6.512A pdb=" N LEU G 54 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE G 83 " --> pdb=" O ILE G 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'G' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 112 through 119 removed outlier: 6.746A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.453A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE4, first strand: chain 'G' and resid 287 through 289 Processing sheet with id=AE5, first strand: chain 'J' and resid 510 through 513 Processing sheet with id=AE6, first strand: chain 'J' and resid 517 through 519 removed outlier: 6.001A pdb=" N ARG J 545 " --> pdb=" O TRP J 554 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP J 554 " --> pdb=" O ARG J 545 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N MET J 555 " --> pdb=" O TYR J 567 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR J 567 " --> pdb=" O MET J 555 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG J 557 " --> pdb=" O GLU J 565 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU J 565 " --> pdb=" O ARG J 557 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 517 through 519 Processing sheet with id=AE8, first strand: chain 'K' and resid 625 through 626 Processing sheet with id=AE9, first strand: chain 'K' and resid 632 through 634 removed outlier: 7.003A pdb=" N LEU K 632 " --> pdb=" O GLU K 727 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP K 657 " --> pdb=" O LEU K 669 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 1971 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: 7.17 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3942 1.32 - 1.46: 6019 1.46 - 1.60: 7456 1.60 - 1.74: 28 1.74 - 1.88: 87 Bond restraints: 17532 Sorted by residual: bond pdb=" CB HIS G 130 " pdb=" CG HIS G 130 " ideal model delta sigma weight residual 1.497 1.351 0.146 1.40e-02 5.10e+03 1.09e+02 bond pdb=" CB HIS C 130 " pdb=" CG HIS C 130 " ideal model delta sigma weight residual 1.497 1.351 0.146 1.40e-02 5.10e+03 1.08e+02 bond pdb=" CB HIS A 130 " pdb=" CG HIS A 130 " ideal model delta sigma weight residual 1.497 1.352 0.145 1.40e-02 5.10e+03 1.08e+02 bond pdb=" CB HIS A 41 " pdb=" CG HIS A 41 " ideal model delta sigma weight residual 1.497 1.401 0.096 1.40e-02 5.10e+03 4.72e+01 bond pdb=" CB HIS C 41 " pdb=" CG HIS C 41 " ideal model delta sigma weight residual 1.497 1.401 0.096 1.40e-02 5.10e+03 4.72e+01 ... (remaining 17527 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.01: 639 106.01 - 113.01: 8408 113.01 - 120.02: 7228 120.02 - 127.02: 7296 127.02 - 134.03: 213 Bond angle restraints: 23784 Sorted by residual: angle pdb=" N THR C 319 " pdb=" CA THR C 319 " pdb=" C THR C 319 " ideal model delta sigma weight residual 114.04 102.11 11.93 1.24e+00 6.50e-01 9.25e+01 angle pdb=" N THR A 319 " pdb=" CA THR A 319 " pdb=" C THR A 319 " ideal model delta sigma weight residual 114.04 102.12 11.92 1.24e+00 6.50e-01 9.24e+01 angle pdb=" N THR G 319 " pdb=" CA THR G 319 " pdb=" C THR G 319 " ideal model delta sigma weight residual 114.04 102.17 11.87 1.24e+00 6.50e-01 9.16e+01 angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.20 -6.54 7.30e-01 1.88e+00 8.02e+01 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.66 126.19 -6.53 7.30e-01 1.88e+00 7.99e+01 ... (remaining 23779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10360 17.88 - 35.75: 228 35.75 - 53.63: 59 53.63 - 71.51: 36 71.51 - 89.39: 9 Dihedral angle restraints: 10692 sinusoidal: 4488 harmonic: 6204 Sorted by residual: dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 278 " pdb=" CB CYS C 278 " ideal model delta sinusoidal sigma weight residual -86.00 -138.99 52.99 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS G 46 " pdb=" SG CYS G 46 " pdb=" SG CYS G 278 " pdb=" CB CYS G 278 " ideal model delta sinusoidal sigma weight residual -86.00 -138.98 52.98 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -138.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 10689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1866 0.101 - 0.203: 584 0.203 - 0.304: 106 0.304 - 0.406: 24 0.406 - 0.507: 24 Chirality restraints: 2604 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.44e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.19e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.06e+01 ... (remaining 2601 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 195 " -0.065 2.00e-02 2.50e+03 3.34e-02 2.23e+01 pdb=" CG TYR A 195 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 195 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 195 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 195 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 195 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 195 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 195 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 195 " 0.065 2.00e-02 2.50e+03 3.33e-02 2.22e+01 pdb=" CG TYR C 195 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 195 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR C 195 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 195 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 195 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR C 195 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 195 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 195 " 0.065 2.00e-02 2.50e+03 3.33e-02 2.22e+01 pdb=" CG TYR G 195 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR G 195 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR G 195 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR G 195 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR G 195 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 195 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 195 " 0.044 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 12 2.48 - 3.09: 11772 3.09 - 3.69: 25768 3.69 - 4.30: 40619 4.30 - 4.90: 65362 Nonbonded interactions: 143533 Sorted by model distance: nonbonded pdb=" OE1 GLN H 611 " pdb=" OH TYR L 671 " model vdw 1.876 2.440 nonbonded pdb=" OE1 GLN H 611 " pdb=" CZ TYR L 671 " model vdw 2.309 3.260 nonbonded pdb=" OD1 ASP B 415 " pdb=" NZ LYS I 413 " model vdw 2.370 2.520 nonbonded pdb=" NZ LYS D 413 " pdb=" OD1 ASP I 415 " model vdw 2.370 2.520 nonbonded pdb=" NZ LYS B 413 " pdb=" OD1 ASP D 415 " model vdw 2.370 2.520 ... (remaining 143528 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 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.000 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 46.730 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.021 0.163 17532 Z= 1.397 Angle : 1.732 11.926 23784 Z= 1.176 Chirality : 0.110 0.507 2604 Planarity : 0.009 0.051 3069 Dihedral : 9.571 89.386 6672 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.17), residues: 2133 helix: 0.69 (0.22), residues: 375 sheet: 0.50 (0.20), residues: 570 loop : 0.38 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.009 TRP G 127 HIS 0.011 0.003 HIS B 472 PHE 0.035 0.007 PHE F 705 TYR 0.065 0.008 TYR A 195 ARG 0.008 0.001 ARG G 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 LYS cc_start: 0.7998 (mttm) cc_final: 0.7577 (mtmm) REVERT: B 412 LYS cc_start: 0.8869 (tttm) cc_final: 0.8658 (mttp) REVERT: H 555 MET cc_start: 0.8295 (mtp) cc_final: 0.8022 (mtp) REVERT: H 614 PRO cc_start: 0.7667 (Cg_endo) cc_final: 0.7191 (Cg_exo) REVERT: L 632 LEU cc_start: 0.5669 (tp) cc_final: 0.5389 (tp) REVERT: L 694 THR cc_start: 0.8251 (m) cc_final: 0.8016 (p) REVERT: C 208 HIS cc_start: 0.8128 (m-70) cc_final: 0.7890 (m-70) REVERT: D 402 LYS cc_start: 0.8020 (mttm) cc_final: 0.7782 (mtmm) REVERT: E 535 THR cc_start: 0.7386 (m) cc_final: 0.7035 (p) REVERT: E 614 PRO cc_start: 0.7830 (Cg_endo) cc_final: 0.7591 (Cg_exo) REVERT: F 632 LEU cc_start: 0.5560 (tp) cc_final: 0.4716 (tp) REVERT: F 687 SER cc_start: 0.7335 (p) cc_final: 0.6892 (m) REVERT: I 389 MET cc_start: 0.8349 (tpp) cc_final: 0.8064 (tpp) REVERT: J 526 LYS cc_start: 0.7121 (tttt) cc_final: 0.6780 (ttpt) REVERT: K 687 SER cc_start: 0.7671 (p) cc_final: 0.7205 (m) REVERT: K 707 LEU cc_start: 0.6814 (mt) cc_final: 0.6604 (mp) REVERT: K 708 TYR cc_start: 0.7473 (m-80) cc_final: 0.7176 (m-80) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3379 time to fit residues: 261.0605 Evaluate side-chains 295 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 401 ASN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN E 510 GLN ** F 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS G 208 HIS I 355 HIS I 401 ASN ** I 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17532 Z= 0.266 Angle : 0.680 9.802 23784 Z= 0.372 Chirality : 0.045 0.168 2604 Planarity : 0.005 0.064 3069 Dihedral : 5.220 32.276 2727 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.80 % Allowed : 7.86 % Favored : 89.34 % 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: 0.41 (0.17), residues: 2133 helix: 1.64 (0.25), residues: 375 sheet: 0.39 (0.23), residues: 465 loop : -0.13 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 351 HIS 0.019 0.002 HIS A 184 PHE 0.020 0.002 PHE B 440 TYR 0.032 0.002 TYR G 102 ARG 0.009 0.001 ARG L 676 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 341 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7140 (mtm-85) REVERT: H 614 PRO cc_start: 0.8296 (Cg_endo) cc_final: 0.8009 (Cg_exo) REVERT: L 687 SER cc_start: 0.8718 (p) cc_final: 0.8304 (m) REVERT: L 694 THR cc_start: 0.8321 (m) cc_final: 0.8113 (p) REVERT: L 713 TYR cc_start: 0.8175 (p90) cc_final: 0.7942 (p90) REVERT: D 402 LYS cc_start: 0.8109 (mttm) cc_final: 0.7880 (mtmm) REVERT: E 584 SER cc_start: 0.8472 (m) cc_final: 0.8057 (p) REVERT: F 687 SER cc_start: 0.8125 (p) cc_final: 0.7689 (m) REVERT: G 9 ILE cc_start: 0.8726 (mt) cc_final: 0.8514 (mt) REVERT: G 301 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8690 (m) REVERT: I 389 MET cc_start: 0.8563 (tpp) cc_final: 0.8048 (tpp) REVERT: J 526 LYS cc_start: 0.7343 (tttt) cc_final: 0.6910 (ttpt) REVERT: K 687 SER cc_start: 0.8173 (p) cc_final: 0.7774 (m) REVERT: K 692 ASP cc_start: 0.4891 (OUTLIER) cc_final: 0.4637 (p0) REVERT: K 707 LEU cc_start: 0.6613 (mt) cc_final: 0.6349 (mp) outliers start: 52 outliers final: 30 residues processed: 364 average time/residue: 0.2818 time to fit residues: 155.2040 Evaluate side-chains 309 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 276 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 272 ASN Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 462 GLU Chi-restraints excluded: chain J residue 553 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 692 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 355 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN K 648 GLN K 659 HIS ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17532 Z= 0.253 Angle : 0.611 8.350 23784 Z= 0.325 Chirality : 0.044 0.176 2604 Planarity : 0.005 0.057 3069 Dihedral : 4.824 28.014 2727 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.85 % Allowed : 9.64 % Favored : 87.51 % 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: 0.16 (0.17), residues: 2133 helix: 1.49 (0.25), residues: 381 sheet: 0.09 (0.23), residues: 504 loop : -0.27 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 153 HIS 0.009 0.002 HIS A 184 PHE 0.021 0.002 PHE B 440 TYR 0.027 0.002 TYR E 610 ARG 0.006 0.001 ARG L 725 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 295 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8728 (m) REVERT: H 584 SER cc_start: 0.8667 (m) cc_final: 0.8387 (p) REVERT: H 614 PRO cc_start: 0.8432 (Cg_endo) cc_final: 0.8178 (Cg_exo) REVERT: L 687 SER cc_start: 0.8683 (p) cc_final: 0.8343 (m) REVERT: L 694 THR cc_start: 0.8439 (m) cc_final: 0.8158 (p) REVERT: L 713 TYR cc_start: 0.8288 (p90) cc_final: 0.8013 (p90) REVERT: D 347 MET cc_start: 0.7828 (ttp) cc_final: 0.7614 (ttp) REVERT: D 402 LYS cc_start: 0.8285 (mttm) cc_final: 0.8008 (mtmm) REVERT: E 584 SER cc_start: 0.8602 (m) cc_final: 0.8234 (p) REVERT: E 600 VAL cc_start: 0.6598 (t) cc_final: 0.6351 (p) REVERT: F 687 SER cc_start: 0.8376 (p) cc_final: 0.7912 (m) REVERT: F 692 ASP cc_start: 0.5232 (t0) cc_final: 0.4965 (p0) REVERT: G 9 ILE cc_start: 0.8781 (mt) cc_final: 0.8580 (mt) REVERT: I 389 MET cc_start: 0.8547 (tpp) cc_final: 0.7881 (tpp) REVERT: J 508 GLN cc_start: 0.5744 (OUTLIER) cc_final: 0.5525 (pp30) REVERT: J 526 LYS cc_start: 0.7366 (tttt) cc_final: 0.6866 (ttpt) REVERT: K 687 SER cc_start: 0.8275 (p) cc_final: 0.7916 (m) REVERT: K 713 TYR cc_start: 0.7981 (p90) cc_final: 0.7673 (p90) outliers start: 53 outliers final: 40 residues processed: 324 average time/residue: 0.2723 time to fit residues: 135.9068 Evaluate side-chains 304 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 262 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 607 SER Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 704 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 552 LEU Chi-restraints excluded: chain J residue 553 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 HIS ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17532 Z= 0.302 Angle : 0.617 9.429 23784 Z= 0.324 Chirality : 0.044 0.161 2604 Planarity : 0.005 0.071 3069 Dihedral : 4.794 34.327 2727 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.88 % Allowed : 10.45 % Favored : 85.68 % 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: -0.00 (0.17), residues: 2133 helix: 1.49 (0.25), residues: 381 sheet: -0.13 (0.23), residues: 507 loop : -0.37 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 153 HIS 0.008 0.001 HIS A 12 PHE 0.022 0.002 PHE D 440 TYR 0.022 0.002 TYR E 610 ARG 0.004 0.001 ARG K 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 284 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7778 (tp30) cc_final: 0.7558 (tp30) REVERT: A 301 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8665 (m) REVERT: B 389 MET cc_start: 0.8535 (tpt) cc_final: 0.8173 (tpt) REVERT: B 471 TYR cc_start: 0.5932 (m-80) cc_final: 0.5713 (m-80) REVERT: H 526 LYS cc_start: 0.7366 (tttt) cc_final: 0.7046 (ttpt) REVERT: H 584 SER cc_start: 0.8649 (m) cc_final: 0.8412 (p) REVERT: H 614 PRO cc_start: 0.8499 (Cg_endo) cc_final: 0.8220 (Cg_exo) REVERT: L 687 SER cc_start: 0.8881 (p) cc_final: 0.8537 (m) REVERT: L 694 THR cc_start: 0.8496 (m) cc_final: 0.8198 (p) REVERT: L 713 TYR cc_start: 0.8324 (p90) cc_final: 0.8111 (p90) REVERT: C 25 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: E 539 TYR cc_start: 0.8352 (m-80) cc_final: 0.8084 (m-80) REVERT: E 584 SER cc_start: 0.8682 (m) cc_final: 0.8298 (p) REVERT: F 687 SER cc_start: 0.8570 (p) cc_final: 0.8174 (m) REVERT: G 9 ILE cc_start: 0.8768 (mt) cc_final: 0.8551 (mt) REVERT: I 389 MET cc_start: 0.8607 (tpp) cc_final: 0.7967 (tpp) REVERT: J 508 GLN cc_start: 0.5717 (OUTLIER) cc_final: 0.5478 (pp30) REVERT: J 526 LYS cc_start: 0.7366 (tttt) cc_final: 0.6783 (ttpp) REVERT: K 687 SER cc_start: 0.8485 (p) cc_final: 0.8102 (m) REVERT: K 692 ASP cc_start: 0.5541 (t0) cc_final: 0.5299 (p0) outliers start: 72 outliers final: 57 residues processed: 320 average time/residue: 0.2618 time to fit residues: 129.8603 Evaluate side-chains 331 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 271 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 607 SER Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 553 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 620 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 523 SER Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 553 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 592 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Chi-restraints excluded: chain K residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 392 GLN I 401 ASN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17532 Z= 0.287 Angle : 0.609 9.174 23784 Z= 0.317 Chirality : 0.044 0.166 2604 Planarity : 0.005 0.072 3069 Dihedral : 4.776 36.525 2727 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.61 % Allowed : 11.79 % Favored : 84.60 % 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: -0.10 (0.18), residues: 2133 helix: 1.55 (0.26), residues: 381 sheet: -0.19 (0.23), residues: 507 loop : -0.49 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 153 HIS 0.007 0.001 HIS A 12 PHE 0.020 0.002 PHE I 440 TYR 0.023 0.002 TYR K 713 ARG 0.005 0.000 ARG K 725 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 281 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7760 (tp30) cc_final: 0.7524 (tp30) REVERT: A 301 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 389 MET cc_start: 0.8450 (tpt) cc_final: 0.8084 (tpt) REVERT: H 526 LYS cc_start: 0.7517 (tttt) cc_final: 0.7162 (ttpt) REVERT: H 584 SER cc_start: 0.8587 (m) cc_final: 0.8377 (p) REVERT: H 614 PRO cc_start: 0.8527 (Cg_endo) cc_final: 0.8256 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8132 (mm) cc_final: 0.7755 (mt) REVERT: L 687 SER cc_start: 0.8884 (p) cc_final: 0.8519 (m) REVERT: L 694 THR cc_start: 0.8510 (m) cc_final: 0.8227 (p) REVERT: D 347 MET cc_start: 0.8283 (ttm) cc_final: 0.8013 (ttm) REVERT: D 433 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 479 MET cc_start: 0.8334 (mmm) cc_final: 0.8086 (mtm) REVERT: E 539 TYR cc_start: 0.8382 (m-80) cc_final: 0.7989 (m-80) REVERT: E 584 SER cc_start: 0.8733 (m) cc_final: 0.8353 (p) REVERT: F 687 SER cc_start: 0.8657 (p) cc_final: 0.8255 (m) REVERT: G 9 ILE cc_start: 0.8794 (mt) cc_final: 0.8580 (mt) REVERT: G 25 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: G 120 ILE cc_start: 0.8267 (tt) cc_final: 0.8037 (tt) REVERT: G 173 GLU cc_start: 0.7739 (tp30) cc_final: 0.7506 (tp30) REVERT: I 389 MET cc_start: 0.8559 (tpp) cc_final: 0.7918 (tpp) REVERT: J 526 LYS cc_start: 0.7315 (tttt) cc_final: 0.6708 (ttpp) REVERT: J 596 ASP cc_start: 0.7716 (t0) cc_final: 0.7514 (t0) REVERT: K 687 SER cc_start: 0.8549 (p) cc_final: 0.8175 (m) REVERT: K 692 ASP cc_start: 0.5657 (t0) cc_final: 0.5431 (p0) outliers start: 67 outliers final: 60 residues processed: 319 average time/residue: 0.2804 time to fit residues: 141.0265 Evaluate side-chains 333 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 271 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 591 SER Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 553 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain E residue 620 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 553 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 592 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN K 664 GLN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17532 Z= 0.368 Angle : 0.653 10.051 23784 Z= 0.337 Chirality : 0.045 0.220 2604 Planarity : 0.005 0.071 3069 Dihedral : 5.020 40.074 2727 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.36 % Allowed : 11.63 % Favored : 84.01 % 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: -0.30 (0.18), residues: 2133 helix: 1.50 (0.26), residues: 381 sheet: -0.32 (0.21), residues: 573 loop : -0.67 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 153 HIS 0.009 0.002 HIS A 12 PHE 0.022 0.002 PHE I 440 TYR 0.026 0.002 TYR L 713 ARG 0.005 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 283 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 311 ARG cc_start: 0.8946 (ttm-80) cc_final: 0.8554 (ttm110) REVERT: B 498 LEU cc_start: 0.8563 (pp) cc_final: 0.8246 (mt) REVERT: H 526 LYS cc_start: 0.7539 (tttt) cc_final: 0.7190 (ttpt) REVERT: H 584 SER cc_start: 0.8662 (m) cc_final: 0.8444 (p) REVERT: H 614 PRO cc_start: 0.8543 (Cg_endo) cc_final: 0.8279 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8137 (mm) cc_final: 0.7807 (mt) REVERT: L 687 SER cc_start: 0.8910 (p) cc_final: 0.8588 (m) REVERT: L 692 ASP cc_start: 0.6013 (t0) cc_final: 0.5739 (p0) REVERT: C 25 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: D 471 TYR cc_start: 0.6703 (m-10) cc_final: 0.6385 (m-80) REVERT: D 498 LEU cc_start: 0.8656 (pp) cc_final: 0.8084 (mt) REVERT: E 539 TYR cc_start: 0.8424 (m-80) cc_final: 0.8003 (m-80) REVERT: E 584 SER cc_start: 0.8721 (m) cc_final: 0.8393 (p) REVERT: F 687 SER cc_start: 0.8719 (p) cc_final: 0.8403 (m) REVERT: F 692 ASP cc_start: 0.6021 (t0) cc_final: 0.5681 (p0) REVERT: G 9 ILE cc_start: 0.8657 (mt) cc_final: 0.8446 (mt) REVERT: G 25 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: G 120 ILE cc_start: 0.8330 (tt) cc_final: 0.8066 (tt) REVERT: G 173 GLU cc_start: 0.7823 (tp30) cc_final: 0.7620 (tp30) REVERT: I 389 MET cc_start: 0.8567 (tpp) cc_final: 0.7939 (tpp) REVERT: J 526 LYS cc_start: 0.7376 (tttt) cc_final: 0.6765 (ttpp) REVERT: J 596 ASP cc_start: 0.7770 (t0) cc_final: 0.7544 (t0) REVERT: K 687 SER cc_start: 0.8618 (p) cc_final: 0.8260 (m) REVERT: K 692 ASP cc_start: 0.5885 (t0) cc_final: 0.5615 (p0) outliers start: 81 outliers final: 69 residues processed: 330 average time/residue: 0.2632 time to fit residues: 134.7880 Evaluate side-chains 340 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 268 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 591 SER Chi-restraints excluded: chain H residue 592 SER Chi-restraints excluded: chain H residue 622 VAL Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain L residue 707 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 553 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain E residue 620 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 523 SER Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 553 GLU Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 592 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 696 THR Chi-restraints excluded: chain K residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 372 GLN ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17532 Z= 0.194 Angle : 0.578 10.149 23784 Z= 0.297 Chirality : 0.043 0.245 2604 Planarity : 0.005 0.062 3069 Dihedral : 4.785 39.287 2727 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.18 % Allowed : 13.25 % Favored : 83.58 % 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: -0.20 (0.18), residues: 2133 helix: 1.63 (0.26), residues: 381 sheet: -0.30 (0.21), residues: 570 loop : -0.60 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 180 HIS 0.007 0.001 HIS K 659 PHE 0.013 0.002 PHE I 440 TYR 0.023 0.001 TYR K 713 ARG 0.009 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8619 (m) REVERT: B 498 LEU cc_start: 0.8479 (pp) cc_final: 0.8262 (mt) REVERT: H 526 LYS cc_start: 0.7501 (tttt) cc_final: 0.7159 (ttpt) REVERT: H 610 TYR cc_start: 0.8274 (m-80) cc_final: 0.8006 (m-80) REVERT: H 614 PRO cc_start: 0.8528 (Cg_endo) cc_final: 0.8231 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8183 (mm) cc_final: 0.7688 (mt) REVERT: L 687 SER cc_start: 0.8890 (p) cc_final: 0.8571 (m) REVERT: L 692 ASP cc_start: 0.6037 (t0) cc_final: 0.5739 (p0) REVERT: C 25 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: C 199 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7555 (p0) REVERT: D 498 LEU cc_start: 0.8623 (pp) cc_final: 0.8071 (mt) REVERT: E 539 TYR cc_start: 0.8335 (m-80) cc_final: 0.7983 (m-80) REVERT: E 584 SER cc_start: 0.8573 (m) cc_final: 0.8361 (p) REVERT: F 687 SER cc_start: 0.8579 (p) cc_final: 0.8249 (m) REVERT: G 25 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: J 526 LYS cc_start: 0.7329 (tttt) cc_final: 0.6835 (ttpt) REVERT: K 687 SER cc_start: 0.8567 (p) cc_final: 0.8220 (m) outliers start: 59 outliers final: 49 residues processed: 307 average time/residue: 0.2672 time to fit residues: 127.4772 Evaluate side-chains 311 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 258 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 592 SER Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 352 TYR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 620 THR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 508 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 592 SER Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain K residue 634 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 HIS D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 17532 Z= 0.471 Angle : 0.714 10.857 23784 Z= 0.369 Chirality : 0.047 0.206 2604 Planarity : 0.006 0.078 3069 Dihedral : 5.322 41.343 2727 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.15 % Allowed : 13.30 % Favored : 82.55 % 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 (0.17), residues: 2133 helix: 1.38 (0.26), residues: 378 sheet: -0.42 (0.21), residues: 558 loop : -0.84 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 153 HIS 0.011 0.002 HIS A 12 PHE 0.024 0.003 PHE I 440 TYR 0.021 0.002 TYR L 713 ARG 0.008 0.001 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 259 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8698 (m) REVERT: B 498 LEU cc_start: 0.8501 (pp) cc_final: 0.8272 (mt) REVERT: H 526 LYS cc_start: 0.7559 (tttt) cc_final: 0.7220 (ttpt) REVERT: H 614 PRO cc_start: 0.8588 (Cg_endo) cc_final: 0.8303 (Cg_exo) REVERT: L 634 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7698 (mt) REVERT: L 687 SER cc_start: 0.8901 (p) cc_final: 0.8617 (m) REVERT: L 692 ASP cc_start: 0.6223 (t0) cc_final: 0.5850 (p0) REVERT: C 25 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: C 199 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8173 (p0) REVERT: D 479 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8011 (mtt) REVERT: D 498 LEU cc_start: 0.8642 (pp) cc_final: 0.8107 (mt) REVERT: E 539 TYR cc_start: 0.8442 (m-80) cc_final: 0.7998 (m-80) REVERT: F 687 SER cc_start: 0.8719 (p) cc_final: 0.8469 (m) REVERT: G 25 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: I 389 MET cc_start: 0.8799 (tpp) cc_final: 0.7495 (tpp) REVERT: K 687 SER cc_start: 0.8724 (p) cc_final: 0.8265 (m) outliers start: 77 outliers final: 67 residues processed: 300 average time/residue: 0.2624 time to fit residues: 123.0836 Evaluate side-chains 323 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 250 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 578 THR Chi-restraints excluded: chain H residue 592 SER Chi-restraints excluded: chain H residue 620 THR Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain L residue 707 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 553 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain E residue 620 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 642 LEU Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 523 SER Chi-restraints excluded: chain J residue 535 THR Chi-restraints excluded: chain J residue 576 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 592 SER Chi-restraints excluded: chain J residue 607 SER Chi-restraints excluded: chain J residue 622 VAL Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 641 THR Chi-restraints excluded: chain K residue 685 SER Chi-restraints excluded: chain K residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.1980 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 0.0870 chunk 113 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 508 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17532 Z= 0.158 Angle : 0.568 9.898 23784 Z= 0.293 Chirality : 0.042 0.151 2604 Planarity : 0.005 0.060 3069 Dihedral : 4.836 39.864 2727 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.64 % Allowed : 15.02 % Favored : 82.34 % 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: -0.23 (0.18), residues: 2133 helix: 1.61 (0.26), residues: 381 sheet: -0.18 (0.22), residues: 555 loop : -0.69 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.008 0.001 HIS K 659 PHE 0.013 0.002 PHE A 213 TYR 0.021 0.001 TYR L 713 ARG 0.007 0.000 ARG F 725 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 286 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8621 (m) REVERT: B 498 LEU cc_start: 0.8489 (pp) cc_final: 0.8285 (mt) REVERT: H 526 LYS cc_start: 0.7498 (tttt) cc_final: 0.7153 (ttpt) REVERT: H 610 TYR cc_start: 0.8316 (m-80) cc_final: 0.8047 (m-80) REVERT: H 614 PRO cc_start: 0.8505 (Cg_endo) cc_final: 0.8192 (Cg_exo) REVERT: L 627 GLN cc_start: 0.6953 (tm-30) cc_final: 0.6709 (tm-30) REVERT: L 634 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7529 (mt) REVERT: L 687 SER cc_start: 0.8741 (p) cc_final: 0.8471 (m) REVERT: C 25 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: C 199 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7585 (p0) REVERT: D 360 GLN cc_start: 0.8832 (mt0) cc_final: 0.8608 (mt0) REVERT: D 498 LEU cc_start: 0.8603 (pp) cc_final: 0.8063 (mt) REVERT: E 539 TYR cc_start: 0.8284 (m-80) cc_final: 0.7944 (m-80) REVERT: F 687 SER cc_start: 0.8542 (p) cc_final: 0.8242 (m) REVERT: G 120 ILE cc_start: 0.7955 (tt) cc_final: 0.7638 (tt) REVERT: I 389 MET cc_start: 0.8655 (tpp) cc_final: 0.7397 (tpp) REVERT: I 433 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7495 (mt-10) REVERT: K 632 LEU cc_start: 0.6570 (tp) cc_final: 0.6233 (mp) REVERT: K 634 LEU cc_start: 0.8192 (mm) cc_final: 0.7884 (mt) REVERT: K 687 SER cc_start: 0.8570 (p) cc_final: 0.8149 (m) outliers start: 49 outliers final: 36 residues processed: 314 average time/residue: 0.2680 time to fit residues: 131.3293 Evaluate side-chains 310 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 270 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 592 SER Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 553 GLU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 553 GLU Chi-restraints excluded: chain J residue 592 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 712 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17532 Z= 0.210 Angle : 0.576 10.317 23784 Z= 0.298 Chirality : 0.043 0.157 2604 Planarity : 0.005 0.047 3069 Dihedral : 4.750 39.301 2727 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.26 % Allowed : 15.78 % Favored : 81.96 % 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: -0.17 (0.18), residues: 2133 helix: 1.67 (0.26), residues: 381 sheet: -0.14 (0.22), residues: 558 loop : -0.66 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.007 0.001 HIS K 659 PHE 0.015 0.002 PHE I 440 TYR 0.024 0.002 TYR L 713 ARG 0.005 0.000 ARG C 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 273 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8637 (m) REVERT: H 526 LYS cc_start: 0.7511 (tttt) cc_final: 0.7164 (ttpt) REVERT: H 610 TYR cc_start: 0.8366 (m-80) cc_final: 0.8092 (m-80) REVERT: H 614 PRO cc_start: 0.8529 (Cg_endo) cc_final: 0.8208 (Cg_exo) REVERT: L 627 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6719 (tm-30) REVERT: L 634 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7549 (mt) REVERT: L 687 SER cc_start: 0.8764 (p) cc_final: 0.8469 (m) REVERT: C 25 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: D 360 GLN cc_start: 0.8838 (mt0) cc_final: 0.8609 (mt0) REVERT: D 498 LEU cc_start: 0.8592 (pp) cc_final: 0.8029 (mt) REVERT: E 539 TYR cc_start: 0.8306 (m-80) cc_final: 0.8020 (m-80) REVERT: E 553 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6518 (mt-10) REVERT: F 687 SER cc_start: 0.8600 (p) cc_final: 0.8355 (m) REVERT: G 120 ILE cc_start: 0.7969 (tt) cc_final: 0.7657 (tt) REVERT: I 389 MET cc_start: 0.8671 (tpp) cc_final: 0.7381 (tpp) REVERT: K 632 LEU cc_start: 0.6529 (tp) cc_final: 0.6213 (mp) REVERT: K 634 LEU cc_start: 0.8241 (mm) cc_final: 0.7907 (mt) REVERT: K 687 SER cc_start: 0.8595 (p) cc_final: 0.8171 (m) outliers start: 42 outliers final: 36 residues processed: 296 average time/residue: 0.2549 time to fit residues: 119.4696 Evaluate side-chains 301 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 261 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 555 MET Chi-restraints excluded: chain H residue 592 SER Chi-restraints excluded: chain H residue 620 THR Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain L residue 633 SER Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 704 ASP Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 553 GLU Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain I residue 352 TYR Chi-restraints excluded: chain I residue 368 GLN Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 553 GLU Chi-restraints excluded: chain J residue 592 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.1980 chunk 51 optimal weight: 0.0970 chunk 153 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 146 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120095 restraints weight = 26842.603| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.13 r_work: 0.3454 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17532 Z= 0.154 Angle : 0.549 10.726 23784 Z= 0.283 Chirality : 0.042 0.152 2604 Planarity : 0.004 0.063 3069 Dihedral : 4.603 38.563 2727 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.32 % Allowed : 15.83 % Favored : 81.85 % 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: -0.04 (0.18), residues: 2133 helix: 1.77 (0.26), residues: 381 sheet: -0.02 (0.22), residues: 558 loop : -0.60 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.008 0.001 HIS K 659 PHE 0.012 0.001 PHE C 118 TYR 0.024 0.001 TYR L 713 ARG 0.003 0.000 ARG F 725 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.55 seconds wall clock time: 72 minutes 30.41 seconds (4350.41 seconds total)