Starting phenix.real_space_refine (version: dev) on Fri Mar 17 09:57:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/03_2023/7ytc_34085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/03_2023/7ytc_34085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/03_2023/7ytc_34085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/03_2023/7ytc_34085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/03_2023/7ytc_34085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/03_2023/7ytc_34085.pdb" } resolution = 3.39 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= 0.006 sd= 0.049 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 Process input model Symmetric amino acids flipped Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B ASP 570": "OD1" <-> "OD2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C ASP 453": "OD1" <-> "OD2" Residue "C PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C GLU 508": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 508": "OE1" <-> "OE2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "E PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "E PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E GLU 526": "OE1" <-> "OE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 532": "OE1" <-> "OE2" Residue "E ASP 553": "OD1" <-> "OD2" Residue "E TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "G GLU 388": "OE1" <-> "OE2" Residue "G PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 491": "NH1" <-> "NH2" Residue "G TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 526": "OE1" <-> "OE2" Residue "G ASP 553": "OD1" <-> "OD2" Residue "G TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 527": "OE1" <-> "OE2" Residue "H GLU 549": "OE1" <-> "OE2" Residue "H TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 104": "OD1" <-> "OD2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 410": "OE1" <-> "OE2" Residue "K PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 483": "OD1" <-> "OD2" Residue "K TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 526": "OE1" <-> "OE2" Residue "K ASP 553": "OD1" <-> "OD2" Residue "L PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L ARG 451": "NH1" <-> "NH2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L GLU 498": "OE1" <-> "OE2" Residue "L TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 508": "OE1" <-> "OE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 526": "OE1" <-> "OE2" Residue "L TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 41": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19328 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 825 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Chain: "K" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.11, per 1000 atoms: 0.57 Number of scatterers: 19328 At special positions: 0 Unit cell: (116.748, 189.612, 163.116, 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 95 16.00 O 3790 8.00 N 3276 7.00 C 12167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.05 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.05 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.04 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.04 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.04 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.01 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.05 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM19284 O5 NAG H 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG J 201 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 3.1 seconds 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4724 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 60 sheets defined 9.4% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.587A pdb=" N ASN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.957A pdb=" N THR A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.606A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.058A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 4.015A pdb=" N GLY B 557 " --> pdb=" O LYS B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.718A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 467 removed outlier: 3.550A pdb=" N ARG C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.799A pdb=" N THR C 530 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 4.267A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'D' and resid 460 through 467 removed outlier: 4.113A pdb=" N LEU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 529 removed outlier: 3.861A pdb=" N TRP D 528 " --> pdb=" O SER D 524 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 529 " --> pdb=" O GLU D 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 529' Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 419 removed outlier: 4.078A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 414 through 419' Processing helix chain 'F' and resid 524 through 529 removed outlier: 3.608A pdb=" N TRP F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 removed outlier: 3.817A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 524 through 530 removed outlier: 4.023A pdb=" N TRP G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN G 529 " --> pdb=" O GLU G 525 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 524 through 530' Processing helix chain 'G' and resid 553 through 557 removed outlier: 3.954A pdb=" N GLY G 557 " --> pdb=" O LYS G 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 415 through 419 removed outlier: 4.192A pdb=" N ASN H 419 " --> pdb=" O ASP H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 530 removed outlier: 3.514A pdb=" N THR H 530 " --> pdb=" O GLU H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 557 removed outlier: 3.590A pdb=" N THR H 556 " --> pdb=" O ASP H 553 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY H 557 " --> pdb=" O LYS H 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 553 through 557' Processing helix chain 'K' and resid 414 through 419 removed outlier: 4.134A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 414 through 419' Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 525 through 529 removed outlier: 3.852A pdb=" N ASN K 529 " --> pdb=" O GLU K 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 525 through 529' Processing helix chain 'L' and resid 353 through 358 removed outlier: 3.673A pdb=" N PHE L 358 " --> pdb=" O PHE L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 420 removed outlier: 4.013A pdb=" N ASN L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 Processing helix chain 'L' and resid 525 through 530 Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.537A pdb=" N ALA A 407 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.586A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 562 through 563 removed outlier: 6.791A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.975A pdb=" N PHE J 60 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 346 through 350 Processing sheet with id=AA9, first strand: chain 'B' and resid 454 through 457 removed outlier: 6.091A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 454 through 457 removed outlier: 6.091A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 485 through 489 Processing sheet with id=AB3, first strand: chain 'C' and resid 346 through 350 Processing sheet with id=AB4, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AB5, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AB6, first strand: chain 'C' and resid 477 through 479 Processing sheet with id=AB7, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB8, first strand: chain 'D' and resid 346 through 350 removed outlier: 4.120A pdb=" N ALA D 407 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.706A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.480A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.480A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC4, first strand: chain 'D' and resid 565 through 567 removed outlier: 7.240A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 346 through 350 Processing sheet with id=AC6, first strand: chain 'E' and resid 379 through 383 removed outlier: 3.656A pdb=" N LEU E 437 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 removed outlier: 3.736A pdb=" N GLN E 493 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AD2, first strand: chain 'F' and resid 379 through 383 Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 457 removed outlier: 4.132A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 4.132A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD6, first strand: chain 'F' and resid 565 through 567 Processing sheet with id=AD7, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.937A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 407 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE G 405 " --> pdb=" O ASP G 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.937A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 379 through 383 Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 Processing sheet with id=AE3, first strand: chain 'G' and resid 493 through 494 removed outlier: 3.816A pdb=" N GLN G 493 " --> pdb=" O GLN G 490 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN G 490 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 346 through 350 Processing sheet with id=AE5, first strand: chain 'H' and resid 379 through 383 removed outlier: 3.742A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.907A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.907A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE9, first strand: chain 'H' and resid 566 through 567 Processing sheet with id=AF1, first strand: chain 'J' and resid 21 through 22 removed outlier: 4.432A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AF3, first strand: chain 'J' and resid 110 through 113 removed outlier: 3.688A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 348 through 350 Processing sheet with id=AF5, first strand: chain 'K' and resid 379 through 384 Processing sheet with id=AF6, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.660A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AF8, first strand: chain 'K' and resid 506 through 507 Processing sheet with id=AF9, first strand: chain 'K' and resid 561 through 562 removed outlier: 6.346A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 346 through 350 Processing sheet with id=AG2, first strand: chain 'L' and resid 380 through 383 removed outlier: 4.090A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 441 " --> pdb=" O PHE L 424 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN L 439 " --> pdb=" O CYS L 426 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 454 through 457 removed outlier: 4.038A pdb=" N GLY L 478 " --> pdb=" O TYR L 515 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 493 through 495 removed outlier: 4.278A pdb=" N TRP L 488 " --> pdb=" O LEU L 495 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 539 " --> pdb=" O PHE L 485 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 33 through 37 removed outlier: 4.203A pdb=" N LEU R 86 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR R 81 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 58 through 62 removed outlier: 5.362A pdb=" N THR R 60 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG R 50 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR R 47 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL R 101 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN R 116 " --> pdb=" O CYS R 104 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1494 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: 6.27 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3154 1.25 - 1.40: 4597 1.40 - 1.54: 11748 1.54 - 1.68: 174 1.68 - 1.83: 129 Bond restraints: 19802 Sorted by residual: bond pdb=" CA ASN H 563 " pdb=" C ASN H 563 " ideal model delta sigma weight residual 1.524 1.389 0.134 1.30e-02 5.92e+03 1.07e+02 bond pdb=" C ASN H 563 " pdb=" O ASN H 563 " ideal model delta sigma weight residual 1.234 1.111 0.123 1.22e-02 6.72e+03 1.02e+02 bond pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 1.520 1.406 0.114 1.20e-02 6.94e+03 9.05e+01 bond pdb=" C ILE J 39 " pdb=" O ILE J 39 " ideal model delta sigma weight residual 1.238 1.137 0.100 1.06e-02 8.90e+03 8.98e+01 bond pdb=" C VAL C 564 " pdb=" O VAL C 564 " ideal model delta sigma weight residual 1.237 1.146 0.091 9.80e-03 1.04e+04 8.59e+01 ... (remaining 19797 not shown) Histogram of bond angle deviations from ideal: 92.25 - 102.44: 112 102.44 - 112.62: 11273 112.62 - 122.81: 13151 122.81 - 132.99: 2509 132.99 - 143.18: 48 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N THR B 533 " pdb=" CA THR B 533 " pdb=" C THR B 533 " ideal model delta sigma weight residual 111.28 133.25 -21.97 1.09e+00 8.42e-01 4.06e+02 angle pdb=" N THR K 533 " pdb=" CA THR K 533 " pdb=" C THR K 533 " ideal model delta sigma weight residual 111.28 127.21 -15.93 1.09e+00 8.42e-01 2.14e+02 angle pdb=" C SER L 496 " pdb=" N PRO L 497 " pdb=" CA PRO L 497 " ideal model delta sigma weight residual 119.87 134.35 -14.48 1.04e+00 9.25e-01 1.94e+02 angle pdb=" C LYS F 558 " pdb=" N PRO F 559 " pdb=" CA PRO F 559 " ideal model delta sigma weight residual 119.05 134.25 -15.20 1.11e+00 8.12e-01 1.88e+02 angle pdb=" N PRO B 452 " pdb=" CA PRO B 452 " pdb=" C PRO B 452 " ideal model delta sigma weight residual 113.84 130.83 -16.99 1.30e+00 5.92e-01 1.71e+02 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10518 17.93 - 35.85: 1029 35.85 - 53.78: 318 53.78 - 71.70: 79 71.70 - 89.63: 21 Dihedral angle restraints: 11965 sinusoidal: 4718 harmonic: 7247 Sorted by residual: dihedral pdb=" C THR F 560 " pdb=" N THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual -122.00 -151.55 29.55 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual 123.40 151.69 -28.29 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C ASN R 85 " pdb=" N ASN R 85 " pdb=" CA ASN R 85 " pdb=" CB ASN R 85 " ideal model delta harmonic sigma weight residual -122.60 -146.78 24.18 0 2.50e+00 1.60e-01 9.36e+01 ... (remaining 11962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 3161 0.270 - 0.540: 51 0.540 - 0.809: 7 0.809 - 1.079: 1 1.079 - 1.349: 1 Chirality restraints: 3221 Sorted by residual: chirality pdb=" CA THR F 560 " pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CB THR F 560 " both_signs ideal model delta sigma weight residual False 2.53 1.18 1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA ASN R 85 " pdb=" N ASN R 85 " pdb=" C ASN R 85 " pdb=" CB ASN R 85 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA THR B 533 " pdb=" N THR B 533 " pdb=" C THR B 533 " pdb=" CB THR B 533 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3218 not shown) Planarity restraints: 3467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 558 " -0.101 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO K 559 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO K 559 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO K 559 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 562 " 0.030 2.00e-02 2.50e+03 5.98e-02 3.57e+01 pdb=" C TYR C 562 " -0.103 2.00e-02 2.50e+03 pdb=" O TYR C 562 " 0.038 2.00e-02 2.50e+03 pdb=" N ASN C 563 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 488 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C TRP B 488 " -0.095 2.00e-02 2.50e+03 pdb=" O TRP B 488 " 0.036 2.00e-02 2.50e+03 pdb=" N MET B 489 " 0.033 2.00e-02 2.50e+03 ... (remaining 3464 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 28 1.95 - 2.68: 1065 2.68 - 3.42: 25865 3.42 - 4.16: 44293 4.16 - 4.90: 76988 Nonbonded interactions: 148239 Sorted by model distance: nonbonded pdb=" NH1 ARG C 384 " pdb=" O ALA C 389 " model vdw 1.208 2.520 nonbonded pdb=" O ARG L 491 " pdb=" NE2 GLN L 493 " model vdw 1.411 2.520 nonbonded pdb=" OD2 ASP E 453 " pdb=" CE2 TYR E 455 " model vdw 1.433 3.340 nonbonded pdb=" OD2 ASP E 453 " pdb=" CZ TYR E 455 " model vdw 1.501 3.260 nonbonded pdb=" OD1 ASN C 386 " pdb=" CG GLU C 388 " model vdw 1.537 3.440 ... (remaining 148234 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' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 12167 2.51 5 N 3276 2.21 5 O 3790 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.600 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: 8.770 Check model and map are aligned: 0.270 Process input model: 51.180 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.011 0.144 19802 Z= 0.698 Angle : 1.322 21.968 27093 Z= 0.828 Chirality : 0.087 1.349 3221 Planarity : 0.008 0.151 3456 Dihedral : 16.461 89.627 7157 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.44 % Rotamer Outliers : 8.45 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 5.24 % 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: -2.42 (0.16), residues: 2438 helix: -2.45 (0.36), residues: 151 sheet: -0.93 (0.17), residues: 897 loop : -2.01 (0.16), residues: 1390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 312 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 186 outliers final: 97 residues processed: 464 average time/residue: 0.3793 time to fit residues: 253.7002 Evaluate side-chains 350 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 253 time to evaluate : 2.512 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 97 outliers final: 3 residues processed: 97 average time/residue: 0.2532 time to fit residues: 43.4011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.0980 chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 73 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 450 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 19802 Z= 0.349 Angle : 0.728 14.440 27093 Z= 0.373 Chirality : 0.051 0.421 3221 Planarity : 0.006 0.084 3456 Dihedral : 5.279 31.544 2649 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.15 % Favored : 90.81 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.16), residues: 2438 helix: -2.37 (0.32), residues: 166 sheet: -0.88 (0.17), residues: 897 loop : -2.07 (0.16), residues: 1375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 279 time to evaluate : 2.346 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 27 residues processed: 309 average time/residue: 0.3933 time to fit residues: 174.9991 Evaluate side-chains 261 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 2.326 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.1929 time to fit residues: 13.0313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 40.0000 chunk 182 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 60 optimal weight: 0.0270 chunk 219 optimal weight: 0.9980 chunk 236 optimal weight: 8.9990 chunk 195 optimal weight: 40.0000 chunk 217 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 439 GLN B 490 GLN B 529 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 HIS ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19802 Z= 0.228 Angle : 0.643 12.029 27093 Z= 0.323 Chirality : 0.048 0.362 3221 Planarity : 0.005 0.068 3456 Dihedral : 4.886 29.131 2649 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.45 % Favored : 91.47 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % 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: -2.20 (0.16), residues: 2438 helix: -2.08 (0.35), residues: 159 sheet: -0.68 (0.17), residues: 894 loop : -1.96 (0.16), residues: 1385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 2.386 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 47 outliers final: 22 residues processed: 289 average time/residue: 0.3691 time to fit residues: 157.0867 Evaluate side-chains 249 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 2.330 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.1693 time to fit residues: 10.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 450 HIS ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 19802 Z= 0.378 Angle : 0.697 13.809 27093 Z= 0.354 Chirality : 0.051 0.396 3221 Planarity : 0.006 0.066 3456 Dihedral : 5.116 27.989 2649 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.84 % Favored : 90.07 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % 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: -2.22 (0.16), residues: 2438 helix: -1.99 (0.36), residues: 157 sheet: -0.68 (0.17), residues: 870 loop : -1.99 (0.16), residues: 1411 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 41 residues processed: 289 average time/residue: 0.3602 time to fit residues: 152.8495 Evaluate side-chains 266 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 2.183 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.1814 time to fit residues: 16.6971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 20.0000 chunk 132 optimal weight: 0.0770 chunk 3 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 161 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 chunk 209 optimal weight: 40.0000 chunk 58 optimal weight: 1.9990 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 ASN ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 19802 Z= 0.328 Angle : 0.667 13.555 27093 Z= 0.337 Chirality : 0.049 0.371 3221 Planarity : 0.005 0.064 3456 Dihedral : 4.990 28.518 2649 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.94 % Favored : 90.98 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % 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: -2.18 (0.17), residues: 2438 helix: -1.83 (0.37), residues: 164 sheet: -0.66 (0.17), residues: 877 loop : -1.97 (0.16), residues: 1397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 232 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 257 average time/residue: 0.3980 time to fit residues: 149.3701 Evaluate side-chains 231 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 2.614 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1769 time to fit residues: 8.7487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 0.6980 chunk 209 optimal weight: 40.0000 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 chunk 57 optimal weight: 0.6980 chunk 233 optimal weight: 0.8980 chunk 193 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19802 Z= 0.185 Angle : 0.618 11.365 27093 Z= 0.307 Chirality : 0.047 0.344 3221 Planarity : 0.005 0.060 3456 Dihedral : 4.675 28.207 2649 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.92 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.17), residues: 2438 helix: -1.69 (0.36), residues: 163 sheet: -0.45 (0.17), residues: 874 loop : -1.82 (0.16), residues: 1401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 271 average time/residue: 0.3834 time to fit residues: 152.2070 Evaluate side-chains 246 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 2.474 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.1755 time to fit residues: 11.1053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 107 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19802 Z= 0.245 Angle : 0.623 11.792 27093 Z= 0.312 Chirality : 0.048 0.369 3221 Planarity : 0.005 0.058 3456 Dihedral : 4.661 28.853 2649 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.65 % Favored : 91.26 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2438 helix: -1.53 (0.37), residues: 168 sheet: -0.46 (0.17), residues: 894 loop : -1.79 (0.17), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 249 average time/residue: 0.3898 time to fit residues: 142.0757 Evaluate side-chains 233 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 222 time to evaluate : 2.303 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1860 time to fit residues: 7.1738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 0.0870 chunk 92 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 69 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 158 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 19802 Z= 0.286 Angle : 0.647 12.200 27093 Z= 0.325 Chirality : 0.048 0.365 3221 Planarity : 0.005 0.057 3456 Dihedral : 4.736 30.269 2649 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.15 % Favored : 90.77 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2438 helix: -1.63 (0.36), residues: 175 sheet: -0.45 (0.17), residues: 890 loop : -1.82 (0.17), residues: 1373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 2.298 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 238 average time/residue: 0.3934 time to fit residues: 136.0073 Evaluate side-chains 230 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 213 time to evaluate : 2.433 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.1750 time to fit residues: 8.8524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 169 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 215 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 overall best weight: 1.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 19802 Z= 0.256 Angle : 0.645 11.993 27093 Z= 0.322 Chirality : 0.048 0.371 3221 Planarity : 0.005 0.056 3456 Dihedral : 4.690 29.171 2649 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2438 helix: -1.55 (0.37), residues: 175 sheet: -0.41 (0.17), residues: 884 loop : -1.77 (0.17), residues: 1379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 239 average time/residue: 0.4018 time to fit residues: 140.7587 Evaluate side-chains 228 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 2.271 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1782 time to fit residues: 7.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 0.0020 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 159 optimal weight: 30.0000 chunk 240 optimal weight: 10.0000 chunk 220 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 chunk 151 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19802 Z= 0.207 Angle : 0.630 11.214 27093 Z= 0.315 Chirality : 0.047 0.348 3221 Planarity : 0.005 0.055 3456 Dihedral : 4.573 28.814 2649 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.08 % Favored : 91.84 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2438 helix: -1.42 (0.37), residues: 174 sheet: -0.32 (0.17), residues: 872 loop : -1.72 (0.17), residues: 1392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 2.364 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 242 average time/residue: 0.3950 time to fit residues: 140.2659 Evaluate side-chains 234 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 2.341 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1805 time to fit residues: 6.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** 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 = 0.4525 r_free = 0.4525 target = 0.203025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125799 restraints weight = 27276.749| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.19 r_work: 0.3372 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3687 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: