Starting phenix.real_space_refine on Sat Feb 17 16:59:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/02_2024/7uhz_26520_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/02_2024/7uhz_26520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/02_2024/7uhz_26520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/02_2024/7uhz_26520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/02_2024/7uhz_26520_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhz_26520/02_2024/7uhz_26520_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 93 5.16 5 C 12180 2.51 5 N 3333 2.21 5 O 3693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 84": "OD1" <-> "OD2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "M ASP 30": "OD1" <-> "OD2" Residue "M PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "N ASP 1": "OD1" <-> "OD2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ASP 30": "OD1" <-> "OD2" Residue "N PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19299 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "N" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "A" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "B" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "C" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Time building chain proxies: 10.43, per 1000 atoms: 0.54 Number of scatterers: 19299 At special positions: 0 Unit cell: (98.175, 103.125, 204.6, 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 93 16.00 O 3693 8.00 N 3333 7.00 C 12180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 3.5 seconds 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4530 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 19.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.130A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.514A pdb=" N ARG H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.130A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.513A pdb=" N ARG I 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.129A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.513A pdb=" N ARG J 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 429 removed outlier: 4.190A pdb=" N GLY A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.296A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 429 removed outlier: 4.191A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.295A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 429 removed outlier: 4.190A pdb=" N GLY C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.295A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 105 through 106 Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 105 through 106 Processing sheet with id=AA5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 105 through 106 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.515A pdb=" N ILE L 52 " --> pdb=" O TRP L 39 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU L 50 " --> pdb=" O GLN L 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.672A pdb=" N ASP L 74 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.514A pdb=" N ILE M 52 " --> pdb=" O TRP M 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN M 41 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU M 50 " --> pdb=" O GLN M 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 19 through 24 removed outlier: 3.672A pdb=" N ASP M 74 " --> pdb=" O SER M 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.514A pdb=" N ILE N 52 " --> pdb=" O TRP N 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN N 41 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU N 50 " --> pdb=" O GLN N 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.673A pdb=" N ASP N 74 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AB7, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.312A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 559 through 563 removed outlier: 7.728A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 368 current: chain 'A' and resid 448 through 457 Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 175 removed outlier: 4.756A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 190 current: chain 'A' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 343 through 346 Processing sheet with id=AC2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AC5, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AC6, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AC7, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.674A pdb=" N PHE A 641 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.696A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.312A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 368 current: chain 'B' and resid 448 through 457 Processing sheet with id=AD2, first strand: chain 'B' and resid 157 through 175 removed outlier: 4.755A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 190 current: chain 'B' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 343 through 346 Processing sheet with id=AD3, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AD4, first strand: chain 'B' and resid 213 through 214 Processing sheet with id=AD5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD6, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AD7, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AD8, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.674A pdb=" N PHE B 641 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.618A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.311A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 368 current: chain 'C' and resid 448 through 457 Processing sheet with id=AE3, first strand: chain 'C' and resid 157 through 175 removed outlier: 4.756A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 190 current: chain 'C' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 343 through 346 Processing sheet with id=AE4, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AE5, first strand: chain 'C' and resid 213 through 214 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE8, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AE9, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.675A pdb=" N PHE C 641 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1461 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: 7.30 Time building geometry restraints manager: 8.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6360 1.34 - 1.46: 4972 1.46 - 1.58: 8303 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 19779 Sorted by residual: bond pdb=" C CYS A 133 " pdb=" N PRO A 134 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.26e-02 6.30e+03 7.18e+00 bond pdb=" C CYS B 133 " pdb=" N PRO B 134 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.26e-02 6.30e+03 7.18e+00 bond pdb=" C CYS C 133 " pdb=" N PRO C 134 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.26e-02 6.30e+03 6.97e+00 bond pdb=" CA SER C 209 " pdb=" C SER C 209 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.41e-02 5.03e+03 6.34e+00 bond pdb=" CA SER A 209 " pdb=" C SER A 209 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.41e-02 5.03e+03 6.19e+00 ... (remaining 19774 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.30: 393 105.30 - 112.48: 9945 112.48 - 119.67: 6039 119.67 - 126.85: 10202 126.85 - 134.04: 283 Bond angle restraints: 26862 Sorted by residual: angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 112.90 107.77 5.13 9.60e-01 1.09e+00 2.85e+01 angle pdb=" N ILE A 154 " pdb=" CA ILE A 154 " pdb=" C ILE A 154 " ideal model delta sigma weight residual 112.90 107.78 5.12 9.60e-01 1.09e+00 2.84e+01 angle pdb=" N ILE C 154 " pdb=" CA ILE C 154 " pdb=" C ILE C 154 " ideal model delta sigma weight residual 112.90 107.83 5.07 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C VAL A 705 " pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 122.06 112.29 9.77 1.86e+00 2.89e-01 2.76e+01 angle pdb=" C VAL B 705 " pdb=" N GLN B 706 " pdb=" CA GLN B 706 " ideal model delta sigma weight residual 122.06 112.34 9.72 1.86e+00 2.89e-01 2.73e+01 ... (remaining 26857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10752 17.70 - 35.40: 840 35.40 - 53.10: 111 53.10 - 70.80: 48 70.80 - 88.50: 12 Dihedral angle restraints: 11763 sinusoidal: 4695 harmonic: 7068 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.58 -53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.56 -53.56 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.55 -53.55 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 11760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2080 0.042 - 0.084: 545 0.084 - 0.126: 229 0.126 - 0.168: 38 0.168 - 0.209: 9 Chirality restraints: 2901 Sorted by residual: chirality pdb=" CB THR C 241 " pdb=" CA THR C 241 " pdb=" OG1 THR C 241 " pdb=" CG2 THR C 241 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR A 241 " pdb=" CA THR A 241 " pdb=" OG1 THR A 241 " pdb=" CG2 THR A 241 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR B 241 " pdb=" CA THR B 241 " pdb=" OG1 THR B 241 " pdb=" CG2 THR B 241 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2898 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 534 " -0.016 2.00e-02 2.50e+03 1.76e-02 4.64e+00 pdb=" CG HIS C 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS C 534 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS C 534 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS C 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 534 " -0.016 2.00e-02 2.50e+03 1.76e-02 4.63e+00 pdb=" CG HIS A 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS A 534 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 534 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS A 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 534 " -0.016 2.00e-02 2.50e+03 1.75e-02 4.61e+00 pdb=" CG HIS B 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 534 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 534 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS B 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 534 " -0.003 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 369 2.61 - 3.18: 18064 3.18 - 3.75: 31481 3.75 - 4.33: 43854 4.33 - 4.90: 72226 Nonbonded interactions: 165994 Sorted by model distance: nonbonded pdb=" ND2 ASN H 58 " pdb=" O SER A 590 " model vdw 2.033 2.520 nonbonded pdb=" O THR A 143 " pdb=" OH TYR A 452 " model vdw 2.096 2.440 nonbonded pdb=" O THR C 143 " pdb=" OH TYR C 452 " model vdw 2.096 2.440 nonbonded pdb=" O THR B 143 " pdb=" OH TYR B 452 " model vdw 2.096 2.440 nonbonded pdb=" NZ LYS A 253 " pdb=" OD1 ASN A 255 " model vdw 2.108 2.520 ... (remaining 165989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.310 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: 19.590 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 54.050 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.120 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 0.065 19779 Z= 0.339 Angle : 0.775 9.772 26862 Z= 0.451 Chirality : 0.046 0.209 2901 Planarity : 0.004 0.034 3498 Dihedral : 13.196 88.496 7170 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.49 (0.17), residues: 2391 helix: -1.02 (0.26), residues: 333 sheet: -1.17 (0.19), residues: 777 loop : -0.74 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 174 HIS 0.020 0.002 HIS B 534 PHE 0.016 0.002 PHE B 223 TYR 0.033 0.002 TYR C 296 ARG 0.018 0.001 ARG C 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7652 (tt0) cc_final: 0.7395 (tt0) REVERT: H 54 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8018 (mp0) REVERT: H 81 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7188 (tp30) REVERT: I 81 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7452 (tp30) REVERT: J 46 GLU cc_start: 0.7872 (tt0) cc_final: 0.7572 (tt0) REVERT: L 2 ILE cc_start: 0.8394 (mt) cc_final: 0.8133 (mp) REVERT: L 5 THR cc_start: 0.7888 (p) cc_final: 0.7684 (p) REVERT: L 43 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8606 (mmtt) REVERT: L 46 GLN cc_start: 0.9056 (pt0) cc_final: 0.8527 (pp30) REVERT: L 49 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8655 (ttpp) REVERT: L 90 TYR cc_start: 0.7403 (m-80) cc_final: 0.7195 (m-80) REVERT: L 101 THR cc_start: 0.8484 (p) cc_final: 0.8174 (p) REVERT: M 27 GLU cc_start: 0.6937 (pm20) cc_final: 0.6660 (pm20) REVERT: M 43 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8321 (mmtt) REVERT: M 46 GLN cc_start: 0.8950 (pt0) cc_final: 0.8625 (pp30) REVERT: N 2 ILE cc_start: 0.8423 (mt) cc_final: 0.8158 (mp) REVERT: N 43 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8627 (mmtt) REVERT: N 46 GLN cc_start: 0.9047 (pt0) cc_final: 0.8639 (pp30) REVERT: N 89 MET cc_start: 0.8201 (tpt) cc_final: 0.7955 (tpt) REVERT: A 169 THR cc_start: 0.9455 (m) cc_final: 0.9218 (p) REVERT: A 183 MET cc_start: 0.5719 (mtm) cc_final: 0.5145 (mmp) REVERT: A 185 ILE cc_start: 0.7534 (mt) cc_final: 0.7234 (pt) REVERT: A 230 THR cc_start: 0.8966 (t) cc_final: 0.8708 (t) REVERT: A 263 HIS cc_start: 0.6734 (m-70) cc_final: 0.6493 (p-80) REVERT: B 214 VAL cc_start: 0.7884 (t) cc_final: 0.7670 (p) REVERT: B 275 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7144 (mt-10) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.3247 time to fit residues: 179.6337 Evaluate side-chains 255 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 100 optimal weight: 0.0030 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 217 optimal weight: 5.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN M 80 HIS ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN B 438 GLN B 507 GLN B 534 HIS C 343 ASN C 710 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19779 Z= 0.206 Angle : 0.634 10.350 26862 Z= 0.330 Chirality : 0.045 0.221 2901 Planarity : 0.004 0.046 3498 Dihedral : 5.048 23.337 2697 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.53 % Allowed : 8.37 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.15 (0.17), residues: 2391 helix: -0.47 (0.26), residues: 318 sheet: -0.93 (0.18), residues: 885 loop : -0.54 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 174 HIS 0.017 0.001 HIS A 534 PHE 0.020 0.002 PHE C 325 TYR 0.028 0.001 TYR C 282 ARG 0.005 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 299 time to evaluate : 2.063 Fit side-chains revert: symmetry clash REVERT: H 18 VAL cc_start: 0.7914 (p) cc_final: 0.7688 (p) REVERT: H 46 GLU cc_start: 0.7714 (tt0) cc_final: 0.7511 (tt0) REVERT: H 81 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6554 (mp0) REVERT: I 23 LYS cc_start: 0.9208 (tptp) cc_final: 0.8838 (tptp) REVERT: I 81 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6772 (mp0) REVERT: J 46 GLU cc_start: 0.7900 (tt0) cc_final: 0.7695 (tt0) REVERT: J 80 MET cc_start: 0.7440 (tpp) cc_final: 0.7159 (tpp) REVERT: J 81 GLU cc_start: 0.7596 (tp30) cc_final: 0.7262 (mp0) REVERT: L 46 GLN cc_start: 0.9024 (pt0) cc_final: 0.8528 (pp30) REVERT: L 106 THR cc_start: 0.8627 (m) cc_final: 0.8083 (p) REVERT: N 43 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8475 (mmtt) REVERT: N 46 GLN cc_start: 0.9011 (pt0) cc_final: 0.8635 (pp30) REVERT: N 106 THR cc_start: 0.8800 (m) cc_final: 0.8510 (p) REVERT: A 185 ILE cc_start: 0.7418 (mt) cc_final: 0.6893 (pt) REVERT: A 195 GLU cc_start: 0.8167 (pp20) cc_final: 0.7833 (pp20) REVERT: B 189 ARG cc_start: 0.6428 (mtp180) cc_final: 0.6014 (mtm180) REVERT: B 214 VAL cc_start: 0.7801 (t) cc_final: 0.7595 (p) outliers start: 32 outliers final: 19 residues processed: 314 average time/residue: 0.2912 time to fit residues: 140.9777 Evaluate side-chains 257 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 238 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 393 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AHIS ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 692 HIS A 710 GLN C 255 ASN C 706 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19779 Z= 0.214 Angle : 0.580 13.426 26862 Z= 0.303 Chirality : 0.043 0.214 2901 Planarity : 0.004 0.067 3498 Dihedral : 4.781 21.970 2697 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.53 % Allowed : 9.95 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.05 (0.17), residues: 2391 helix: -0.12 (0.26), residues: 318 sheet: -0.97 (0.18), residues: 924 loop : -0.45 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 174 HIS 0.015 0.001 HIS L 80 PHE 0.018 0.001 PHE A 325 TYR 0.021 0.001 TYR A 179 ARG 0.013 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 279 time to evaluate : 2.399 Fit side-chains REVERT: H 80 MET cc_start: 0.6065 (mmm) cc_final: 0.5836 (mmm) REVERT: H 81 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6511 (mp0) REVERT: I 23 LYS cc_start: 0.9182 (tptp) cc_final: 0.8762 (tptp) REVERT: I 81 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6858 (mp0) REVERT: J 80 MET cc_start: 0.7493 (tpp) cc_final: 0.7160 (tpp) REVERT: L 37 MET cc_start: 0.9060 (tpp) cc_final: 0.8839 (mmm) REVERT: L 43 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8698 (mmtt) REVERT: L 46 GLN cc_start: 0.9014 (pt0) cc_final: 0.8456 (pp30) REVERT: M 43 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8618 (mmtt) REVERT: N 37 MET cc_start: 0.9168 (mmm) cc_final: 0.8776 (mmm) REVERT: A 195 GLU cc_start: 0.8087 (pp20) cc_final: 0.7729 (pp20) REVERT: A 200 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7817 (mtmm) REVERT: A 550 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9079 (mp) REVERT: B 183 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.4683 (mtm) REVERT: B 187 GLU cc_start: 0.8086 (pp20) cc_final: 0.7719 (pp20) REVERT: C 711 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8183 (mt) outliers start: 53 outliers final: 30 residues processed: 307 average time/residue: 0.3004 time to fit residues: 143.0988 Evaluate side-chains 271 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 chunk 114 optimal weight: 0.0670 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 692 HIS C 433 HIS ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19779 Z= 0.172 Angle : 0.565 9.665 26862 Z= 0.293 Chirality : 0.042 0.198 2901 Planarity : 0.004 0.043 3498 Dihedral : 4.571 23.435 2697 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.30 % Allowed : 12.43 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2391 helix: 0.08 (0.26), residues: 330 sheet: -0.82 (0.18), residues: 882 loop : -0.39 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 174 HIS 0.012 0.001 HIS L 80 PHE 0.017 0.001 PHE C 262 TYR 0.018 0.001 TYR B 282 ARG 0.007 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 260 time to evaluate : 2.129 Fit side-chains revert: symmetry clash REVERT: I 23 LYS cc_start: 0.9149 (tptp) cc_final: 0.8720 (tptp) REVERT: J 46 GLU cc_start: 0.8175 (tt0) cc_final: 0.7822 (tt0) REVERT: L 37 MET cc_start: 0.9071 (tpp) cc_final: 0.8824 (mmm) REVERT: M 43 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8704 (mmtt) REVERT: N 37 MET cc_start: 0.9190 (mmm) cc_final: 0.8803 (mmm) REVERT: A 195 GLU cc_start: 0.8033 (pp20) cc_final: 0.7695 (pp20) REVERT: A 550 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9019 (mp) REVERT: B 187 GLU cc_start: 0.8086 (pp20) cc_final: 0.7710 (pp20) REVERT: C 711 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8122 (mt) outliers start: 48 outliers final: 30 residues processed: 281 average time/residue: 0.3021 time to fit residues: 131.7551 Evaluate side-chains 264 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 232 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.3980 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS A 692 HIS B 343 ASN B 433 HIS ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19779 Z= 0.345 Angle : 0.604 7.877 26862 Z= 0.317 Chirality : 0.044 0.196 2901 Planarity : 0.004 0.047 3498 Dihedral : 4.692 24.596 2697 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.44 % Allowed : 12.77 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2391 helix: 0.12 (0.26), residues: 330 sheet: -0.85 (0.18), residues: 846 loop : -0.40 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 50 HIS 0.035 0.002 HIS A 692 PHE 0.017 0.002 PHE C 262 TYR 0.025 0.002 TYR H 59 ARG 0.005 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 241 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 23 LYS cc_start: 0.9127 (tptp) cc_final: 0.8685 (tptp) REVERT: J 80 MET cc_start: 0.7562 (tpp) cc_final: 0.7148 (tpp) REVERT: A 195 GLU cc_start: 0.8152 (pp20) cc_final: 0.7861 (pp20) REVERT: A 200 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7877 (mtmm) REVERT: A 550 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8983 (mp) REVERT: C 200 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7393 (pttp) REVERT: C 711 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8303 (mt) outliers start: 72 outliers final: 49 residues processed: 276 average time/residue: 0.3067 time to fit residues: 131.8174 Evaluate side-chains 277 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 226 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 57 optimal weight: 0.1980 chunk 232 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 681 HIS ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19779 Z= 0.178 Angle : 0.569 9.104 26862 Z= 0.293 Chirality : 0.042 0.211 2901 Planarity : 0.004 0.050 3498 Dihedral : 4.460 21.563 2697 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.82 % Allowed : 13.68 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2391 helix: 0.32 (0.27), residues: 333 sheet: -0.78 (0.18), residues: 849 loop : -0.37 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.010 0.001 HIS A 534 PHE 0.015 0.001 PHE C 262 TYR 0.015 0.001 TYR C 179 ARG 0.004 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 254 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.5890 (mmm) cc_final: 0.5054 (tpp) REVERT: I 10 GLU cc_start: 0.7113 (mp0) cc_final: 0.6767 (mp0) REVERT: I 23 LYS cc_start: 0.9121 (tptp) cc_final: 0.8669 (tptp) REVERT: I 33 ASP cc_start: 0.7800 (m-30) cc_final: 0.7342 (m-30) REVERT: J 46 GLU cc_start: 0.8294 (tt0) cc_final: 0.8027 (tt0) REVERT: J 81 GLU cc_start: 0.7925 (tp30) cc_final: 0.7696 (tp30) REVERT: L 37 MET cc_start: 0.9175 (mmm) cc_final: 0.8880 (mmm) REVERT: L 46 GLN cc_start: 0.9086 (pt0) cc_final: 0.8624 (pp30) REVERT: M 82 MET cc_start: 0.6823 (tmm) cc_final: 0.6514 (tmm) REVERT: A 195 GLU cc_start: 0.8060 (pp20) cc_final: 0.7771 (pp20) REVERT: A 242 ARG cc_start: 0.7696 (ppt170) cc_final: 0.7451 (ppt170) REVERT: A 366 MET cc_start: 0.8544 (mmm) cc_final: 0.7715 (mmm) REVERT: A 421 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7819 (mtp) REVERT: A 550 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8944 (mp) REVERT: B 182 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6587 (t80) REVERT: B 242 ARG cc_start: 0.7510 (ppt170) cc_final: 0.7251 (ppt170) REVERT: C 183 MET cc_start: 0.5658 (ptt) cc_final: 0.5017 (mmt) REVERT: C 711 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8276 (mt) outliers start: 59 outliers final: 34 residues processed: 287 average time/residue: 0.3144 time to fit residues: 138.5210 Evaluate side-chains 263 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 19779 Z= 0.525 Angle : 0.699 9.238 26862 Z= 0.369 Chirality : 0.047 0.256 2901 Planarity : 0.005 0.046 3498 Dihedral : 4.988 22.905 2697 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 3.16 % Allowed : 14.16 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.07 (0.17), residues: 2391 helix: -0.07 (0.27), residues: 333 sheet: -1.09 (0.18), residues: 813 loop : -0.48 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 539 HIS 0.026 0.002 HIS A 534 PHE 0.017 0.002 PHE A 287 TYR 0.023 0.002 TYR C 179 ARG 0.012 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 235 time to evaluate : 2.394 Fit side-chains REVERT: H 80 MET cc_start: 0.6457 (mmm) cc_final: 0.5907 (tpp) REVERT: I 10 GLU cc_start: 0.7203 (mp0) cc_final: 0.6854 (mp0) REVERT: I 23 LYS cc_start: 0.9093 (tptp) cc_final: 0.8600 (tptp) REVERT: I 33 ASP cc_start: 0.7979 (m-30) cc_final: 0.7434 (m-30) REVERT: L 37 MET cc_start: 0.9332 (mmm) cc_final: 0.8561 (mmm) REVERT: M 82 MET cc_start: 0.6960 (tmm) cc_final: 0.6622 (tmm) REVERT: A 550 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8922 (mp) REVERT: B 195 GLU cc_start: 0.8108 (pp20) cc_final: 0.7823 (pp20) REVERT: B 366 MET cc_start: 0.8552 (mmm) cc_final: 0.7761 (mmm) REVERT: C 183 MET cc_start: 0.5777 (ptt) cc_final: 0.5340 (mmt) REVERT: C 711 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8405 (mt) outliers start: 66 outliers final: 44 residues processed: 270 average time/residue: 0.3050 time to fit residues: 128.9351 Evaluate side-chains 268 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 222 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 181 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 534 HIS ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19779 Z= 0.186 Angle : 0.603 9.844 26862 Z= 0.311 Chirality : 0.042 0.232 2901 Planarity : 0.004 0.049 3498 Dihedral : 4.636 22.906 2697 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.39 % Allowed : 15.35 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2391 helix: -0.22 (0.26), residues: 369 sheet: -0.94 (0.18), residues: 849 loop : -0.28 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.008 0.001 HIS L 80 PHE 0.019 0.001 PHE C 294 TYR 0.019 0.001 TYR C 179 ARG 0.007 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 247 time to evaluate : 1.996 Fit side-chains revert: symmetry clash REVERT: H 40 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7894 (ttp80) REVERT: H 80 MET cc_start: 0.6519 (mmm) cc_final: 0.6002 (tpp) REVERT: I 23 LYS cc_start: 0.9105 (tptp) cc_final: 0.8634 (tptp) REVERT: I 33 ASP cc_start: 0.7874 (m-30) cc_final: 0.7439 (m-30) REVERT: M 82 MET cc_start: 0.6887 (tmm) cc_final: 0.6561 (tmm) REVERT: A 195 GLU cc_start: 0.8027 (pp20) cc_final: 0.7800 (pp20) REVERT: A 242 ARG cc_start: 0.7589 (ppt170) cc_final: 0.7138 (ppt170) REVERT: A 550 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8896 (mp) REVERT: B 182 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6461 (t80) REVERT: B 366 MET cc_start: 0.8392 (mmm) cc_final: 0.7698 (mmm) REVERT: C 711 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8393 (mt) outliers start: 50 outliers final: 35 residues processed: 277 average time/residue: 0.3014 time to fit residues: 128.3496 Evaluate side-chains 265 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 227 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19779 Z= 0.228 Angle : 0.607 9.785 26862 Z= 0.313 Chirality : 0.043 0.196 2901 Planarity : 0.004 0.042 3498 Dihedral : 4.589 20.758 2697 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.39 % Allowed : 15.88 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2391 helix: -0.22 (0.26), residues: 369 sheet: -0.88 (0.18), residues: 846 loop : -0.25 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 50 HIS 0.010 0.001 HIS L 80 PHE 0.019 0.001 PHE B 294 TYR 0.026 0.001 TYR C 179 ARG 0.005 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 236 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: H 80 MET cc_start: 0.6519 (mmm) cc_final: 0.6202 (tpp) REVERT: I 23 LYS cc_start: 0.9087 (tptp) cc_final: 0.8640 (tptp) REVERT: I 33 ASP cc_start: 0.7901 (m-30) cc_final: 0.7379 (m-30) REVERT: I 80 MET cc_start: 0.6871 (mmm) cc_final: 0.5668 (mmm) REVERT: L 46 GLN cc_start: 0.9029 (pt0) cc_final: 0.8576 (pp30) REVERT: M 82 MET cc_start: 0.6932 (tmm) cc_final: 0.6604 (tmm) REVERT: A 195 GLU cc_start: 0.8049 (pp20) cc_final: 0.7812 (pp20) REVERT: A 550 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8872 (mp) REVERT: B 182 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6464 (t80) REVERT: B 366 MET cc_start: 0.8425 (mmm) cc_final: 0.7727 (mmm) REVERT: C 711 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8341 (mt) outliers start: 50 outliers final: 36 residues processed: 264 average time/residue: 0.3175 time to fit residues: 131.6635 Evaluate side-chains 267 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 534 HIS ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19779 Z= 0.199 Angle : 0.608 9.819 26862 Z= 0.311 Chirality : 0.043 0.201 2901 Planarity : 0.004 0.043 3498 Dihedral : 4.520 20.494 2697 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.30 % Allowed : 16.07 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2391 helix: -0.22 (0.26), residues: 369 sheet: -0.82 (0.18), residues: 852 loop : -0.19 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 50 HIS 0.012 0.001 HIS L 80 PHE 0.018 0.001 PHE B 294 TYR 0.025 0.001 TYR C 179 ARG 0.005 0.000 ARG A 494 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 237 time to evaluate : 2.581 Fit side-chains revert: symmetry clash REVERT: H 80 MET cc_start: 0.6908 (mmm) cc_final: 0.6406 (tpt) REVERT: I 23 LYS cc_start: 0.9093 (tptp) cc_final: 0.8620 (tptp) REVERT: I 33 ASP cc_start: 0.7889 (m-30) cc_final: 0.7412 (m-30) REVERT: L 37 MET cc_start: 0.9272 (mmm) cc_final: 0.8524 (mmm) REVERT: L 46 GLN cc_start: 0.9024 (pt0) cc_final: 0.8615 (pp30) REVERT: M 82 MET cc_start: 0.6936 (tmm) cc_final: 0.6612 (tmm) REVERT: M 96 LYS cc_start: 0.9013 (tttm) cc_final: 0.8568 (tttm) REVERT: A 242 ARG cc_start: 0.7671 (ppt170) cc_final: 0.7141 (ppt170) REVERT: A 254 TYR cc_start: 0.8288 (t80) cc_final: 0.8022 (t80) REVERT: A 550 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8875 (mp) REVERT: B 182 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6532 (t80) REVERT: B 366 MET cc_start: 0.8384 (mmm) cc_final: 0.7706 (mmm) REVERT: C 294 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6626 (m-10) REVERT: C 711 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8292 (mt) outliers start: 48 outliers final: 35 residues processed: 266 average time/residue: 0.2980 time to fit residues: 123.7262 Evaluate side-chains 263 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 224 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 0.0770 chunk 195 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82AHIS ** I 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074129 restraints weight = 53055.950| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.14 r_work: 0.3104 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19779 Z= 0.341 Angle : 0.643 9.767 26862 Z= 0.333 Chirality : 0.044 0.203 2901 Planarity : 0.004 0.041 3498 Dihedral : 4.628 20.838 2697 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.10 % Allowed : 16.55 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2391 helix: -0.19 (0.26), residues: 351 sheet: -0.86 (0.18), residues: 828 loop : -0.20 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 50 HIS 0.011 0.001 HIS L 80 PHE 0.018 0.002 PHE C 294 TYR 0.033 0.001 TYR C 179 ARG 0.005 0.000 ARG A 494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.10 seconds wall clock time: 76 minutes 53.73 seconds (4613.73 seconds total)