Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 09:25:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/04_2023/7sco_25040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/04_2023/7sco_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_25040/04_2023/7sco_25040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/04_2023/7sco_25040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/04_2023/7sco_25040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sco_25040/04_2023/7sco_25040.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 8.96, 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: 7.15 Conformation dependent library (CDL) restraints added in 2.6 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: 1.30 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: 6.77 Time building geometry restraints manager: 7.67 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: 9985 17.88 - 35.75: 225 35.75 - 53.63: 59 53.63 - 71.51: 36 71.51 - 89.39: 9 Dihedral angle restraints: 10314 sinusoidal: 4110 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 10311 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: 3.230 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: 8.650 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 46.350 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.140 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.420 ------------------------------------------------------------------------------- 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 : 9.757 89.386 6294 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 % 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 *********************** 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 : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3465 time to fit residues: 267.7487 Evaluate side-chains 285 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8930 ------------------------------------------------------------------------------- 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: 0.6980 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: 6.9990 chunk 100 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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** K 659 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 17532 Z= 0.253 Angle : 0.677 8.111 23784 Z= 0.368 Chirality : 0.046 0.197 2604 Planarity : 0.005 0.064 3069 Dihedral : 5.206 32.201 2349 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 2.85 % 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: 0.40 (0.17), residues: 2133 helix: 1.60 (0.25), residues: 375 sheet: 0.40 (0.23), residues: 465 loop : -0.13 (0.16), residues: 1293 *********************** 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 389 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 336 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 359 average time/residue: 0.2918 time to fit residues: 158.6713 Evaluate side-chains 304 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 274 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1614 time to fit residues: 11.8287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 17532 Z= 0.289 Angle : 0.631 8.326 23784 Z= 0.336 Chirality : 0.044 0.305 2604 Planarity : 0.005 0.069 3069 Dihedral : 4.867 27.674 2349 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.88 % 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: 0.19 (0.18), residues: 2133 helix: 1.43 (0.25), residues: 381 sheet: 0.17 (0.21), residues: 561 loop : -0.26 (0.18), residues: 1191 *********************** 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 329 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 294 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 28 residues processed: 315 average time/residue: 0.2750 time to fit residues: 133.7709 Evaluate side-chains 290 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1537 time to fit residues: 10.8872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 191 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 392 GLN I 401 ASN J 508 GLN J 510 GLN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17532 Z= 0.236 Angle : 0.586 9.172 23784 Z= 0.307 Chirality : 0.043 0.210 2604 Planarity : 0.005 0.064 3069 Dihedral : 4.644 23.714 2349 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.05 % 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: 0.15 (0.18), residues: 2133 helix: 1.53 (0.26), residues: 381 sheet: -0.03 (0.21), residues: 567 loop : -0.24 (0.18), residues: 1185 *********************** 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 322 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 299 average time/residue: 0.2771 time to fit residues: 128.3835 Evaluate side-chains 290 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 263 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1662 time to fit residues: 11.5267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 HIS D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN J 510 GLN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 17532 Z= 0.302 Angle : 0.619 8.210 23784 Z= 0.322 Chirality : 0.044 0.190 2604 Planarity : 0.005 0.067 3069 Dihedral : 4.644 23.395 2349 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.62 % 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: -0.03 (0.18), residues: 2133 helix: 1.52 (0.26), residues: 381 sheet: -0.05 (0.23), residues: 495 loop : -0.45 (0.17), residues: 1257 *********************** 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 313 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 283 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 298 average time/residue: 0.2690 time to fit residues: 124.0357 Evaluate side-chains 293 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 273 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1559 time to fit residues: 8.4076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS D 392 GLN G 141 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 17532 Z= 0.463 Angle : 0.718 8.542 23784 Z= 0.373 Chirality : 0.047 0.228 2604 Planarity : 0.006 0.076 3069 Dihedral : 4.997 21.794 2349 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.83 % 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: -0.43 (0.17), residues: 2133 helix: 1.31 (0.26), residues: 381 sheet: -0.25 (0.22), residues: 540 loop : -0.80 (0.17), residues: 1212 *********************** 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 310 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 27 residues processed: 294 average time/residue: 0.2802 time to fit residues: 127.6117 Evaluate side-chains 290 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 263 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1613 time to fit residues: 10.9077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 123 optimal weight: 0.0470 chunk 93 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 HIS D 392 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 510 GLN ** K 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17532 Z= 0.182 Angle : 0.581 9.885 23784 Z= 0.300 Chirality : 0.043 0.245 2604 Planarity : 0.005 0.064 3069 Dihedral : 4.608 23.537 2349 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.92 % 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: -0.19 (0.18), residues: 2133 helix: 1.56 (0.26), residues: 381 sheet: -0.07 (0.22), residues: 537 loop : -0.68 (0.17), residues: 1215 *********************** 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 290 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 281 average time/residue: 0.3126 time to fit residues: 138.4787 Evaluate side-chains 266 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 254 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1743 time to fit residues: 6.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 17532 Z= 0.408 Angle : 0.672 10.981 23784 Z= 0.349 Chirality : 0.046 0.361 2604 Planarity : 0.005 0.076 3069 Dihedral : 4.850 22.788 2349 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2133 helix: 1.41 (0.26), residues: 381 sheet: -0.26 (0.22), residues: 549 loop : -0.80 (0.17), residues: 1203 *********************** 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 284 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 21 residues processed: 267 average time/residue: 0.2825 time to fit residues: 117.3472 Evaluate side-chains 274 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2318 time to fit residues: 13.4435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.0770 chunk 176 optimal weight: 0.5980 chunk 188 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 508 GLN D 392 GLN ** F 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 17532 Z= 0.175 Angle : 0.573 10.156 23784 Z= 0.297 Chirality : 0.043 0.324 2604 Planarity : 0.005 0.070 3069 Dihedral : 4.596 23.434 2349 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.70 % 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: -0.21 (0.18), residues: 2133 helix: 1.57 (0.26), residues: 381 sheet: -0.03 (0.22), residues: 543 loop : -0.74 (0.17), residues: 1209 *********************** 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 288 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 275 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 282 average time/residue: 0.2913 time to fit residues: 128.8886 Evaluate side-chains 268 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1684 time to fit residues: 5.8081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17532 Z= 0.201 Angle : 0.578 10.471 23784 Z= 0.300 Chirality : 0.043 0.280 2604 Planarity : 0.005 0.053 3069 Dihedral : 4.482 22.834 2349 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.16 % 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: -0.13 (0.18), residues: 2133 helix: 1.67 (0.26), residues: 381 sheet: -0.03 (0.24), residues: 486 loop : -0.65 (0.17), residues: 1266 ********************** 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 269 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 268 average time/residue: 0.2741 time to fit residues: 115.4624 Evaluate side-chains 260 residues out of total 1857 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 258 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1650 time to fit residues: 3.2216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116772 restraints weight = 26982.197| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.15 r_work: 0.3407 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5329 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= 0.276 Angle : 0.609 10.543 23784 Z= 0.316 Chirality : 0.044 0.293 2604 Planarity : 0.005 0.081 3069 Dihedral : 4.600 22.816 2349 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.32 % 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: 1.56 (0.26), residues: 381 sheet: 0.10 (0.24), residues: 477 loop : -0.72 (0.17), residues: 1275 =============================================================================== Job complete usr+sys time: 3856.27 seconds wall clock time: 71 minutes 5.79 seconds (4265.79 seconds total)