Starting phenix.real_space_refine on Sat Nov 18 05:04:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/11_2023/7ytd_34086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/11_2023/7ytd_34086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/11_2023/7ytd_34086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/11_2023/7ytd_34086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/11_2023/7ytd_34086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytd_34086/11_2023/7ytd_34086.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.030 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 116 5.16 5 C 13645 2.51 5 N 3696 2.21 5 O 4236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 4": "NH1" <-> "NH2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Residue "U GLU 51": "OE1" <-> "OE2" Residue "U GLU 96": "OE1" <-> "OE2" Residue "V GLU 28": "OE1" <-> "OE2" Residue "V TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21693 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 18, 'TRANS': 210} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} 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: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 18, 'TRANS': 206} 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: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 1 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: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "J" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 834 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} 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: "S" 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: "U" 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: "V" 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: "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: 11.62, per 1000 atoms: 0.54 Number of scatterers: 21693 At special positions: 0 Unit cell: (121.716, 187.128, 164.772, 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 116 16.00 O 4236 8.00 N 3696 7.00 C 13645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.05 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=1.99 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=1.88 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 37 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 49 " - pdb=" SG CYS S 58 " distance=2.02 Simple disulfide: pdb=" SG CYS U 37 " - pdb=" SG CYS U 104 " distance=2.03 Simple disulfide: pdb=" SG CYS U 49 " - pdb=" SG CYS U 58 " distance=2.03 Simple disulfide: pdb=" SG CYS V 37 " - pdb=" SG CYS V 104 " distance=2.03 Simple disulfide: pdb=" SG CYS V 49 " - pdb=" SG CYS V 58 " 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 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 K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 9.09 Conformation dependent library (CDL) restraints added in 4.2 seconds 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5284 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 65 sheets defined 11.2% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.933A pdb=" N LEU A 466 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.585A pdb=" N TRP A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.678A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 462 through 467 removed outlier: 4.111A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 467' Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.785A pdb=" N TRP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.817A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 removed outlier: 4.103A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 removed outlier: 3.530A pdb=" N LEU D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.812A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 removed outlier: 3.850A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 414 through 419' Processing helix chain 'E' and resid 462 through 467 removed outlier: 4.193A pdb=" N LEU E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 467' Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 419 removed outlier: 4.015A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.995A 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 462 through 466 removed outlier: 3.696A pdb=" N ASN F 465 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 466 " --> pdb=" O GLN F 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 462 through 466' Processing helix chain 'F' and resid 524 through 531 removed outlier: 3.546A pdb=" N TRP F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 removed outlier: 3.882A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.545A pdb=" N ASN G 465 " --> pdb=" O GLU G 462 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G 466 " --> pdb=" O GLN G 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 462 through 466' Processing helix chain 'G' and resid 524 through 531 removed outlier: 3.813A pdb=" N TRP G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 557 removed outlier: 3.527A pdb=" N THR G 556 " --> pdb=" O ASP G 553 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY G 557 " --> pdb=" O LYS G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 557' Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 462 through 466 removed outlier: 3.510A pdb=" N ASN H 465 " --> pdb=" O GLU H 462 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 466 " --> pdb=" O GLN H 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 462 through 466' Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'J' and resid 65 through 69 removed outlier: 3.714A pdb=" N CYS J 68 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS J 69 " --> pdb=" O ASP J 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 69' Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.706A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 removed outlier: 3.663A pdb=" N ASN K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 525 through 531 removed outlier: 4.260A pdb=" N ASN K 529 " --> pdb=" O GLU K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 558 removed outlier: 3.896A pdb=" N GLY K 557 " --> pdb=" O ASP K 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 358 Processing helix chain 'L' and resid 414 through 418 removed outlier: 3.946A pdb=" N TRP L 418 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.551A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 531 Processing helix chain 'R' and resid 109 through 113 Processing helix chain 'U' and resid 69 through 73 removed outlier: 3.567A pdb=" N LYS U 73 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 113 removed outlier: 3.662A pdb=" N GLY U 113 " --> pdb=" O ASN U 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 109 through 113' Processing helix chain 'V' and resid 109 through 113 removed outlier: 3.602A pdb=" N GLY V 113 " --> pdb=" O ASN V 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 109 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.667A pdb=" N ALA A 407 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 6.903A 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 removed outlier: 6.314A pdb=" N HIS A 430 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 435 " --> pdb=" O HIS A 430 " (cutoff:3.500A) 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 Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 569 Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.777A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 365 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 381 through 383 removed outlier: 4.127A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 437 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 381 through 383 Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.549A pdb=" N GLY B 478 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.549A pdb=" N GLY B 478 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 350 removed outlier: 5.305A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 404 " --> pdb=" O HIS C 400 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 346 through 350 Processing sheet with id=AB6, first strand: chain 'C' and resid 380 through 383 Processing sheet with id=AB7, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG C 514 " --> pdb=" O GLU C 508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC1, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.739A pdb=" N ALA D 407 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.575A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.065A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.065A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC6, first strand: chain 'E' and resid 346 through 350 removed outlier: 5.763A pdb=" N THR E 366 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ALA E 411 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E 372 " --> pdb=" O PHE E 405 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.661A pdb=" N ASP E 453 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.661A pdb=" N ASP E 453 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 485 through 489 Processing sheet with id=AD2, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AD3, first strand: chain 'F' and resid 379 through 383 Processing sheet with id=AD4, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.545A pdb=" N ILE F 472 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.545A pdb=" N ILE F 472 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD7, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.284A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.539A pdb=" N GLY G 409 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 407 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE G 405 " --> pdb=" O ASP G 371 " (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 removed outlier: 5.332A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.332A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 493 through 494 removed outlier: 3.528A pdb=" N GLN G 493 " --> pdb=" O GLN G 490 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.651A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU H 437 " --> pdb=" O VAL H 428 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 455 through 457 removed outlier: 3.647A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE8, first strand: chain 'H' and resid 506 through 507 Processing sheet with id=AE9, first strand: chain 'J' and resid 40 through 41 removed outlier: 3.577A pdb=" N VAL J 41 " --> pdb=" O VAL L 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'J' and resid 110 through 113 Processing sheet with id=AF2, first strand: chain 'K' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'K' and resid 378 through 384 Processing sheet with id=AF4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.581A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.581A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 485 through 489 Processing sheet with id=AF7, first strand: chain 'K' and resid 564 through 565 Processing sheet with id=AF8, first strand: chain 'L' and resid 346 through 350 removed outlier: 3.823A pdb=" N ASP L 371 " --> pdb=" O PHE L 405 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 381 through 384 removed outlier: 3.564A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.797A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.797A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AG4, first strand: chain 'R' and resid 33 through 38 Processing sheet with id=AG5, first strand: chain 'R' and resid 57 through 62 removed outlier: 6.939A pdb=" N LEU R 48 " --> pdb=" O VAL R 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL R 101 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR R 102 " --> pdb=" O LYS R 117 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS R 117 " --> pdb=" O TYR R 102 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS R 104 " --> pdb=" O THR R 115 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 33 through 38 Processing sheet with id=AG7, first strand: chain 'S' and resid 57 through 62 removed outlier: 7.069A pdb=" N LEU S 48 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS S 104 " --> pdb=" O GLN S 116 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN S 116 " --> pdb=" O CYS S 104 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 33 through 38 Processing sheet with id=AG9, first strand: chain 'U' and resid 57 through 63 removed outlier: 7.029A pdb=" N LEU U 48 " --> pdb=" O VAL U 61 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER U 63 " --> pdb=" O ILE U 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE U 46 " --> pdb=" O SER U 63 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL U 101 " --> pdb=" O GLU U 51 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR U 102 " --> pdb=" O LYS U 117 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS U 117 " --> pdb=" O TYR U 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS U 104 " --> pdb=" O THR U 115 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 33 through 38 Processing sheet with id=AH2, first strand: chain 'V' and resid 57 through 62 removed outlier: 7.071A pdb=" N LEU V 48 " --> pdb=" O VAL V 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS V 104 " --> pdb=" O THR V 115 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 9.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3549 1.31 - 1.44: 5882 1.44 - 1.57: 12606 1.57 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 22196 Sorted by residual: bond pdb=" C ASN V 85 " pdb=" N LEU V 86 " ideal model delta sigma weight residual 1.331 1.552 -0.221 1.41e-02 5.03e+03 2.47e+02 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.541 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C THR L 574 " pdb=" N CYS L 575 " ideal model delta sigma weight residual 1.329 1.421 -0.092 1.40e-02 5.10e+03 4.28e+01 bond pdb=" C SER A 569 " pdb=" N ASP A 570 " ideal model delta sigma weight residual 1.333 1.402 -0.069 1.39e-02 5.18e+03 2.47e+01 bond pdb=" CA TYR C 455 " pdb=" C TYR C 455 " ideal model delta sigma weight residual 1.520 1.467 0.052 1.12e-02 7.97e+03 2.19e+01 ... (remaining 22191 not shown) Histogram of bond angle deviations from ideal: 97.61 - 104.92: 612 104.92 - 112.23: 11726 112.23 - 119.54: 7071 119.54 - 126.85: 10531 126.85 - 134.16: 374 Bond angle restraints: 30314 Sorted by residual: angle pdb=" C ASN V 85 " pdb=" N LEU V 86 " pdb=" CA LEU V 86 " ideal model delta sigma weight residual 122.59 99.67 22.92 1.57e+00 4.06e-01 2.13e+02 angle pdb=" C THR L 574 " pdb=" N CYS L 575 " pdb=" CA CYS L 575 " ideal model delta sigma weight residual 121.70 105.63 16.07 1.80e+00 3.09e-01 7.97e+01 angle pdb=" CA SER A 569 " pdb=" C SER A 569 " pdb=" O SER A 569 " ideal model delta sigma weight residual 121.44 111.32 10.12 1.17e+00 7.31e-01 7.48e+01 angle pdb=" N VAL V 122 " pdb=" CA VAL V 122 " pdb=" C VAL V 122 " ideal model delta sigma weight residual 110.30 118.08 -7.78 9.70e-01 1.06e+00 6.44e+01 angle pdb=" N SER A 569 " pdb=" CA SER A 569 " pdb=" C SER A 569 " ideal model delta sigma weight residual 109.52 120.57 -11.05 1.55e+00 4.16e-01 5.09e+01 ... (remaining 30309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12092 17.99 - 35.97: 1028 35.97 - 53.96: 262 53.96 - 71.94: 54 71.94 - 89.93: 21 Dihedral angle restraints: 13457 sinusoidal: 5334 harmonic: 8123 Sorted by residual: dihedral pdb=" CB CYS R 49 " pdb=" SG CYS R 49 " pdb=" SG CYS R 58 " pdb=" CB CYS R 58 " ideal model delta sinusoidal sigma weight residual -86.00 -159.92 73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS V 49 " pdb=" SG CYS V 49 " pdb=" SG CYS V 58 " pdb=" CB CYS V 58 " ideal model delta sinusoidal sigma weight residual -86.00 -155.64 69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS U 49 " pdb=" SG CYS U 49 " pdb=" SG CYS U 58 " pdb=" CB CYS U 58 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 13454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.395: 3588 0.395 - 0.791: 9 0.791 - 1.186: 1 1.186 - 1.581: 0 1.581 - 1.977: 2 Chirality restraints: 3600 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 563 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -0.42 -1.98 2.00e-01 2.50e+01 9.77e+01 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -0.54 -1.86 2.00e-01 2.50e+01 8.65e+01 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 563 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.51e+01 ... (remaining 3597 not shown) Planarity restraints: 3873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.068 2.00e-02 2.50e+03 6.35e-02 5.04e+01 pdb=" CG ASN K 563 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET K 489 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C MET K 489 " 0.073 2.00e-02 2.50e+03 pdb=" O MET K 489 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN K 490 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 563 " 0.030 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN C 563 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN C 563 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 563 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.039 2.00e-02 2.50e+03 ... (remaining 3870 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 30 1.93 - 2.67: 844 2.67 - 3.42: 30776 3.42 - 4.16: 51572 4.16 - 4.90: 87931 Nonbonded interactions: 171153 Sorted by model distance: nonbonded pdb=" CE1 HIS E 450 " pdb=" NH2 ARG E 514 " model vdw 1.188 3.340 nonbonded pdb=" N TYR V 81 " pdb=" O LEU V 86 " model vdw 1.252 2.520 nonbonded pdb=" O VAL U 23 " pdb=" CB LEU U 120 " model vdw 1.262 3.440 nonbonded pdb=" OG1 THR J 102 " pdb=" N CYS L 575 " model vdw 1.331 2.520 nonbonded pdb=" CD1 ILE J 17 " pdb=" CA ILE J 37 " model vdw 1.332 3.890 ... (remaining 171148 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)) } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.020 Extract box with map and model: 8.110 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 59.130 Find NCS groups from input model: 1.770 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.005 0.221 22196 Z= 0.338 Angle : 0.963 22.918 30314 Z= 0.558 Chirality : 0.079 1.977 3600 Planarity : 0.006 0.092 3863 Dihedral : 14.785 89.926 8071 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 29.57 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.59 % Favored : 90.50 % Rotamer: Outliers : 4.37 % Allowed : 2.63 % Favored : 93.00 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 1.97 % 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: -1.91 (0.16), residues: 2737 helix: -0.88 (0.37), residues: 180 sheet: -0.96 (0.16), residues: 1037 loop : -1.52 (0.16), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 388 time to evaluate : 2.711 Fit side-chains revert: symmetry clash 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 73 residues processed: 472 average time/residue: 0.3404 time to fit residues: 243.5099 Evaluate side-chains 346 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 273 time to evaluate : 2.580 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 3 residues processed: 73 average time/residue: 0.2260 time to fit residues: 32.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 204 optimal weight: 0.4980 chunk 113 optimal weight: 40.0000 chunk 69 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 157 optimal weight: 40.0000 chunk 245 optimal weight: 10.0000 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN F 419 ASN ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN J 29 ASN L 400 HIS L 463 GLN ** U 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 HIS V 123 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 22196 Z= 0.364 Angle : 0.780 17.122 30314 Z= 0.392 Chirality : 0.052 0.597 3600 Planarity : 0.005 0.083 3863 Dihedral : 5.535 43.166 2983 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.22 % Favored : 91.71 % Rotamer: Outliers : 2.43 % Allowed : 13.39 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.96 (0.16), residues: 2737 helix: -1.15 (0.32), residues: 218 sheet: -1.01 (0.16), residues: 1055 loop : -1.50 (0.16), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 295 time to evaluate : 2.702 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 revert: symmetry clash outliers start: 60 outliers final: 41 residues processed: 335 average time/residue: 0.3275 time to fit residues: 173.2919 Evaluate side-chains 304 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 2.826 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: 0.2150 time to fit residues: 20.1186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 245 optimal weight: 0.7980 chunk 265 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 243 optimal weight: 0.0070 chunk 83 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN F 465 ASN ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22196 Z= 0.191 Angle : 0.692 12.727 30314 Z= 0.343 Chirality : 0.049 0.667 3600 Planarity : 0.005 0.085 3863 Dihedral : 5.111 39.232 2983 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.09 % Favored : 92.88 % Rotamer: Outliers : 1.94 % Allowed : 15.82 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.84 (0.16), residues: 2737 helix: -0.78 (0.33), residues: 219 sheet: -0.85 (0.16), residues: 1043 loop : -1.55 (0.16), residues: 1475 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 305 time to evaluate : 2.742 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 revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 340 average time/residue: 0.3342 time to fit residues: 179.6994 Evaluate side-chains 289 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 267 time to evaluate : 2.590 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: 0.2192 time to fit residues: 12.1863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 246 optimal weight: 0.0040 chunk 260 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22196 Z= 0.172 Angle : 0.669 11.425 30314 Z= 0.328 Chirality : 0.048 0.553 3600 Planarity : 0.004 0.083 3863 Dihedral : 4.852 37.089 2983 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.06 % Allowed : 18.04 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.69 (0.16), residues: 2737 helix: -0.76 (0.33), residues: 230 sheet: -0.67 (0.16), residues: 1036 loop : -1.50 (0.16), residues: 1471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 292 time to evaluate : 2.594 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 revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 331 average time/residue: 0.3152 time to fit residues: 166.2829 Evaluate side-chains 293 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.772 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: 0.2116 time to fit residues: 14.2656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 133 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 65 optimal weight: 0.0570 overall best weight: 3.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22196 Z= 0.342 Angle : 0.723 16.088 30314 Z= 0.359 Chirality : 0.049 0.431 3600 Planarity : 0.005 0.082 3863 Dihedral : 5.057 39.026 2983 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.63 % Allowed : 19.62 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.64 (0.16), residues: 2737 helix: -0.70 (0.33), residues: 222 sheet: -0.78 (0.16), residues: 1048 loop : -1.34 (0.16), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 266 time to evaluate : 2.462 Fit side-chains 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 revert: symmetry clash outliers start: 65 outliers final: 42 residues processed: 310 average time/residue: 0.3189 time to fit residues: 157.5087 Evaluate side-chains 285 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 2.579 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 42 outliers final: 1 residues processed: 42 average time/residue: 0.1929 time to fit residues: 18.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 chunk 216 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22196 Z= 0.296 Angle : 0.711 13.653 30314 Z= 0.352 Chirality : 0.048 0.496 3600 Planarity : 0.005 0.083 3863 Dihedral : 5.069 39.585 2983 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.82 % Allowed : 20.95 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.64 (0.16), residues: 2737 helix: -0.68 (0.33), residues: 224 sheet: -0.76 (0.16), residues: 1050 loop : -1.36 (0.16), residues: 1463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 2.735 Fit side-chains revert: symmetry clash 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 revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 21 residues processed: 294 average time/residue: 0.3401 time to fit residues: 160.0983 Evaluate side-chains 265 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 2.609 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.2081 time to fit residues: 11.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 0.0000 chunk 29 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 190 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 260 optimal weight: 0.0370 chunk 162 optimal weight: 9.9990 chunk 158 optimal weight: 0.0020 chunk 120 optimal weight: 1.9990 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22196 Z= 0.173 Angle : 0.686 14.669 30314 Z= 0.334 Chirality : 0.047 0.456 3600 Planarity : 0.004 0.082 3863 Dihedral : 4.759 35.787 2983 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.33 % Allowed : 22.05 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.46 (0.16), residues: 2737 helix: -0.77 (0.33), residues: 225 sheet: -0.48 (0.16), residues: 1031 loop : -1.34 (0.16), residues: 1481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 286 time to evaluate : 2.686 Fit side-chains revert: symmetry clash 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: 33 outliers final: 20 residues processed: 309 average time/residue: 0.3211 time to fit residues: 158.6924 Evaluate side-chains 277 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 257 time to evaluate : 2.725 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.1931 time to fit residues: 10.8909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 177 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 40.0000 chunk 204 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22196 Z= 0.187 Angle : 0.684 12.983 30314 Z= 0.335 Chirality : 0.048 0.624 3600 Planarity : 0.004 0.082 3863 Dihedral : 4.704 35.078 2983 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.85 % Allowed : 23.75 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.38 (0.16), residues: 2737 helix: -0.50 (0.33), residues: 230 sheet: -0.42 (0.16), residues: 1047 loop : -1.34 (0.16), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 277 time to evaluate : 2.670 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 revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 285 average time/residue: 0.3212 time to fit residues: 145.9990 Evaluate side-chains 272 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 2.568 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2030 time to fit residues: 8.7762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 0.0060 chunk 249 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 219 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 487 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22196 Z= 0.233 Angle : 0.698 12.725 30314 Z= 0.344 Chirality : 0.047 0.552 3600 Planarity : 0.005 0.083 3863 Dihedral : 4.743 35.657 2983 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.93 % Allowed : 23.91 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.37 (0.16), residues: 2737 helix: -0.44 (0.33), residues: 230 sheet: -0.42 (0.16), residues: 1029 loop : -1.33 (0.16), residues: 1478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 2.591 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 revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 270 average time/residue: 0.3151 time to fit residues: 136.4032 Evaluate side-chains 258 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 247 time to evaluate : 2.591 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: 0.2241 time to fit residues: 7.7027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 0.1980 chunk 268 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 214 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 chunk 165 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22196 Z= 0.194 Angle : 0.698 14.699 30314 Z= 0.343 Chirality : 0.047 0.536 3600 Planarity : 0.005 0.082 3863 Dihedral : 4.708 34.986 2983 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.53 % Allowed : 24.72 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.28 (0.16), residues: 2737 helix: -0.34 (0.34), residues: 224 sheet: -0.33 (0.16), residues: 1013 loop : -1.28 (0.16), residues: 1500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 268 time to evaluate : 2.676 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 revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 272 average time/residue: 0.3347 time to fit residues: 143.9258 Evaluate side-chains 266 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 257 time to evaluate : 2.864 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2140 time to fit residues: 6.9493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.1980 chunk 228 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.117005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077757 restraints weight = 76097.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080597 restraints weight = 42483.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.080438 restraints weight = 28208.811| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22196 Z= 0.291 Angle : 0.728 12.996 30314 Z= 0.360 Chirality : 0.048 0.563 3600 Planarity : 0.005 0.083 3863 Dihedral : 4.875 36.117 2983 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.53 % Allowed : 25.00 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % 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: -1.35 (0.16), residues: 2737 helix: -0.33 (0.34), residues: 225 sheet: -0.47 (0.16), residues: 1024 loop : -1.28 (0.16), residues: 1488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4681.54 seconds wall clock time: 86 minutes 17.70 seconds (5177.70 seconds total)