Starting phenix.real_space_refine on Sat Jan 20 05:18:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uye_20947/01_2024/6uye_20947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uye_20947/01_2024/6uye_20947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uye_20947/01_2024/6uye_20947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uye_20947/01_2024/6uye_20947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uye_20947/01_2024/6uye_20947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uye_20947/01_2024/6uye_20947.pdb" } resolution = 3.96 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= 0.074 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 51 5.16 5 C 8676 2.51 5 N 2262 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13692 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1808 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 12, 'TRANS': 218} Chain breaks: 2 Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 730 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1808 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 12, 'TRANS': 218} Chain breaks: 2 Chain: "E" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 730 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1808 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 12, 'TRANS': 218} Chain breaks: 2 Chain: "F" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 730 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.15, per 1000 atoms: 0.52 Number of scatterers: 13692 At special positions: 0 Unit cell: (120.51, 122.57, 123.6, 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 51 16.00 O 2703 8.00 N 2262 7.00 C 8676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 301 " - " ASN A 228 " " NAG A 309 " - " ASN A 238 " " NAG B 301 " - " ASN B 228 " " NAG B 309 " - " ASN B 238 " " NAG C 301 " - " ASN C 228 " " NAG C 309 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN A 268 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN B 257 " " NAG Q 1 " - " ASN B 268 " " NAG R 1 " - " ASN E 563 " " NAG S 1 " - " ASN C 257 " " NAG T 1 " - " ASN C 268 " " NAG U 1 " - " ASN F 563 " Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.2 seconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 15.1% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 553 through 575 removed outlier: 3.711A pdb=" N ASN D 563 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.582A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.636A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.724A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.224A pdb=" N SER J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 553 through 575 removed outlier: 3.711A pdb=" N ASN E 563 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.581A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.635A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.724A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.223A pdb=" N SER K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 553 through 575 removed outlier: 3.711A pdb=" N ASN F 563 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.582A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.636A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.724A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.224A pdb=" N SER L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 3.702A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 184 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 64 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.601A pdb=" N GLY A 87 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 89 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 161 removed outlier: 6.580A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 114 removed outlier: 6.549A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 142 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 14.972A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU A 235 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 242 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.500A pdb=" N LEU G 18 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 81 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.088A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.457A pdb=" N CYS G 96 " --> pdb=" O TRP G 121 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP G 121 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS G 98 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.574A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.488A pdb=" N VAL J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.701A pdb=" N ILE B 38 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 184 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 64 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 89 removed outlier: 3.601A pdb=" N GLY B 87 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 89 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 160 through 161 removed outlier: 6.562A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'B' and resid 108 through 114 removed outlier: 6.549A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 142 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 14.971A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 235 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 242 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.500A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.088A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.458A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.575A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.487A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 45 removed outlier: 3.702A pdb=" N ILE C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 184 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 64 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.601A pdb=" N GLY C 87 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 89 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 160 through 161 removed outlier: 6.580A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AC7, first strand: chain 'C' and resid 108 through 114 removed outlier: 6.549A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 142 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 14.971A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU C 235 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 242 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.500A pdb=" N LEU I 18 " --> pdb=" O MET I 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.088A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.457A pdb=" N CYS I 96 " --> pdb=" O TRP I 121 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP I 121 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS I 98 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.575A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.487A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1143 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: 4.51 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2433 1.32 - 1.44: 3874 1.44 - 1.56: 7622 1.56 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 13998 Sorted by residual: bond pdb=" CA HIS H 35 " pdb=" CB HIS H 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.14e+00 bond pdb=" CA HIS G 35 " pdb=" CB HIS G 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.09e+00 bond pdb=" CA HIS I 35 " pdb=" CB HIS I 35 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.60e-02 3.91e+03 5.07e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 13993 not shown) Histogram of bond angle deviations from ideal: 99.89 - 107.14: 480 107.14 - 114.38: 8144 114.38 - 121.63: 7004 121.63 - 128.87: 3263 128.87 - 136.12: 108 Bond angle restraints: 18999 Sorted by residual: angle pdb=" C ASP A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 120.43 125.49 -5.06 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C ASP B 78 " pdb=" N VAL B 79 " pdb=" CA VAL B 79 " ideal model delta sigma weight residual 120.43 125.48 -5.05 9.60e-01 1.09e+00 2.77e+01 angle pdb=" C ASP C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta sigma weight residual 120.43 125.44 -5.01 9.60e-01 1.09e+00 2.73e+01 angle pdb=" C SER G 113 " pdb=" N TYR G 114 " pdb=" CA TYR G 114 " ideal model delta sigma weight residual 122.17 114.35 7.82 1.54e+00 4.22e-01 2.58e+01 angle pdb=" C SER H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta sigma weight residual 122.17 114.40 7.77 1.54e+00 4.22e-01 2.55e+01 ... (remaining 18994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 8244 21.54 - 43.07: 195 43.07 - 64.61: 39 64.61 - 86.14: 45 86.14 - 107.68: 24 Dihedral angle restraints: 8547 sinusoidal: 3729 harmonic: 4818 Sorted by residual: dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 138.49 41.51 0 5.00e+00 4.00e-02 6.89e+01 dihedral pdb=" CA PHE J 94 " pdb=" C PHE J 94 " pdb=" N PRO J 95 " pdb=" CA PRO J 95 " ideal model delta harmonic sigma weight residual 180.00 138.50 41.50 0 5.00e+00 4.00e-02 6.89e+01 dihedral pdb=" CA PHE K 94 " pdb=" C PHE K 94 " pdb=" N PRO K 95 " pdb=" CA PRO K 95 " ideal model delta harmonic sigma weight residual 180.00 138.51 41.49 0 5.00e+00 4.00e-02 6.89e+01 ... (remaining 8544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1545 0.059 - 0.118: 525 0.118 - 0.178: 105 0.178 - 0.237: 18 0.237 - 0.296: 12 Chirality restraints: 2205 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2202 not shown) Planarity restraints: 2385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " 0.061 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO L 95 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE K 94 " 0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO K 95 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 94 " 0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO J 95 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO J 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO J 95 " 0.051 5.00e-02 4.00e+02 ... (remaining 2382 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3466 2.79 - 3.32: 11173 3.32 - 3.84: 22703 3.84 - 4.37: 24183 4.37 - 4.90: 42826 Nonbonded interactions: 104351 Sorted by model distance: nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.260 2.440 nonbonded pdb=" O ILE K 2 " pdb=" OG1 THR K 97 " model vdw 2.261 2.440 nonbonded pdb=" O ILE J 2 " pdb=" OG1 THR J 97 " model vdw 2.261 2.440 nonbonded pdb=" ND2 ASN C 278 " pdb=" O TRP I 108 " model vdw 2.299 2.520 nonbonded pdb=" O ALA D 562 " pdb=" OG1 THR D 566 " model vdw 2.323 2.440 ... (remaining 104346 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 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 5.870 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 36.620 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.010 0.069 13998 Z= 0.665 Angle : 1.115 11.117 18999 Z= 0.601 Chirality : 0.063 0.296 2205 Planarity : 0.007 0.092 2370 Dihedral : 13.541 107.679 5430 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -3.06 (0.18), residues: 1644 helix: -2.26 (0.28), residues: 171 sheet: -1.62 (0.20), residues: 591 loop : -2.27 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP C 104 HIS 0.013 0.002 HIS I 35 PHE 0.027 0.004 PHE C 176 TYR 0.030 0.004 TYR B 109 ARG 0.014 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8364 (p0) cc_final: 0.7976 (p0) REVERT: A 235 GLU cc_start: 0.8108 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 291 TRP cc_start: 0.6138 (p90) cc_final: 0.5447 (p90) REVERT: D 587 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7998 (ttm-80) REVERT: G 34 MET cc_start: 0.8211 (mmm) cc_final: 0.7912 (mmm) REVERT: G 54 ASP cc_start: 0.8402 (p0) cc_final: 0.8104 (p0) REVERT: G 68 PHE cc_start: 0.6834 (m-10) cc_final: 0.6295 (m-80) REVERT: G 119 ASP cc_start: 0.8208 (p0) cc_final: 0.7945 (p0) REVERT: J 28 ASP cc_start: 0.8110 (t0) cc_final: 0.7885 (t0) REVERT: J 37 GLN cc_start: 0.8406 (tt0) cc_final: 0.7811 (tm-30) REVERT: J 104 LEU cc_start: 0.8964 (tp) cc_final: 0.8746 (tt) REVERT: J 108 ARG cc_start: 0.3432 (mtt180) cc_final: 0.1297 (ttp80) REVERT: B 117 ASP cc_start: 0.8377 (p0) cc_final: 0.8055 (p0) REVERT: B 229 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7500 (pp20) REVERT: B 235 GLU cc_start: 0.8125 (tt0) cc_final: 0.7733 (tm-30) REVERT: B 280 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7528 (mp0) REVERT: B 291 TRP cc_start: 0.6110 (p90) cc_final: 0.5466 (p90) REVERT: E 587 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7826 (ttm-80) REVERT: E 588 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7823 (mmmm) REVERT: H 36 TRP cc_start: 0.7741 (m100) cc_final: 0.6682 (m100) REVERT: H 54 ASP cc_start: 0.8415 (p0) cc_final: 0.7919 (p0) REVERT: H 57 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8409 (tptt) REVERT: H 68 PHE cc_start: 0.6897 (m-10) cc_final: 0.6268 (m-80) REVERT: H 119 ASP cc_start: 0.8366 (p0) cc_final: 0.8152 (p0) REVERT: K 37 GLN cc_start: 0.8513 (tt0) cc_final: 0.8167 (tm-30) REVERT: K 71 PHE cc_start: 0.7910 (m-10) cc_final: 0.7667 (m-10) REVERT: K 108 ARG cc_start: 0.3098 (mtt180) cc_final: 0.0693 (ptt90) REVERT: C 56 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7268 (mmmt) REVERT: C 117 ASP cc_start: 0.8384 (p0) cc_final: 0.8087 (p0) REVERT: C 235 GLU cc_start: 0.8120 (tt0) cc_final: 0.7645 (tm-30) REVERT: C 291 TRP cc_start: 0.6106 (p90) cc_final: 0.5472 (p90) REVERT: F 527 ILE cc_start: 0.5793 (mm) cc_final: 0.5114 (mm) REVERT: F 587 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7924 (ttm-80) REVERT: I 34 MET cc_start: 0.8244 (mmm) cc_final: 0.7844 (mmm) REVERT: I 36 TRP cc_start: 0.7700 (m100) cc_final: 0.6711 (m100) REVERT: I 38 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7728 (ttm-80) REVERT: I 54 ASP cc_start: 0.8389 (p0) cc_final: 0.7895 (p0) REVERT: I 94 TYR cc_start: 0.6507 (m-10) cc_final: 0.6283 (m-10) REVERT: I 104 TYR cc_start: 0.8253 (m-10) cc_final: 0.7954 (m-10) REVERT: L 49 TYR cc_start: 0.8000 (p90) cc_final: 0.7555 (p90) REVERT: L 67 SER cc_start: 0.7996 (t) cc_final: 0.7448 (p) REVERT: L 71 PHE cc_start: 0.7798 (m-10) cc_final: 0.7208 (m-10) REVERT: L 108 ARG cc_start: 0.3197 (mtt180) cc_final: 0.0520 (ptt90) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.3143 time to fit residues: 223.7730 Evaluate side-chains 324 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS D 595 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS E 595 GLN K 38 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13998 Z= 0.222 Angle : 0.720 8.563 18999 Z= 0.364 Chirality : 0.047 0.175 2205 Planarity : 0.005 0.051 2370 Dihedral : 12.541 82.628 2451 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.55 % Allowed : 12.08 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 1644 helix: 0.10 (0.40), residues: 174 sheet: -1.42 (0.19), residues: 642 loop : -1.58 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 121 HIS 0.004 0.001 HIS D 516 PHE 0.017 0.002 PHE L 71 TYR 0.026 0.002 TYR H 115 ARG 0.008 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 376 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7480 (mmmt) cc_final: 0.6955 (mptt) REVERT: A 117 ASP cc_start: 0.8403 (p0) cc_final: 0.8022 (p0) REVERT: A 235 GLU cc_start: 0.8059 (tt0) cc_final: 0.7442 (tm-30) REVERT: A 291 TRP cc_start: 0.5837 (p90) cc_final: 0.5313 (p90) REVERT: D 587 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8093 (ttm110) REVERT: G 34 MET cc_start: 0.8162 (mmm) cc_final: 0.7827 (mmm) REVERT: G 54 ASP cc_start: 0.8292 (p0) cc_final: 0.7883 (p0) REVERT: G 57 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8114 (mmmm) REVERT: G 119 ASP cc_start: 0.8294 (p0) cc_final: 0.7700 (t70) REVERT: J 4 MET cc_start: 0.7032 (ttm) cc_final: 0.6567 (ttm) REVERT: J 70 ASP cc_start: 0.8330 (t70) cc_final: 0.8009 (t70) REVERT: J 90 GLN cc_start: 0.8673 (pp30) cc_final: 0.8056 (pp30) REVERT: J 104 LEU cc_start: 0.9041 (tp) cc_final: 0.8645 (tt) REVERT: J 108 ARG cc_start: 0.3408 (mtt180) cc_final: 0.1426 (ptt90) REVERT: B 56 LYS cc_start: 0.7441 (mmmt) cc_final: 0.7062 (mptt) REVERT: B 117 ASP cc_start: 0.8409 (p0) cc_final: 0.8038 (p0) REVERT: B 235 GLU cc_start: 0.8218 (tt0) cc_final: 0.7610 (tm-30) REVERT: B 291 TRP cc_start: 0.6034 (p90) cc_final: 0.5651 (p90) REVERT: E 587 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7858 (ttm-80) REVERT: H 36 TRP cc_start: 0.7632 (m100) cc_final: 0.5920 (m100) REVERT: H 54 ASP cc_start: 0.8381 (p0) cc_final: 0.7808 (p0) REVERT: H 57 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8233 (mmtp) REVERT: H 119 ASP cc_start: 0.8469 (p0) cc_final: 0.7823 (t70) REVERT: K 4 MET cc_start: 0.7228 (ttm) cc_final: 0.6637 (ttm) REVERT: K 90 GLN cc_start: 0.8779 (pp30) cc_final: 0.8065 (pp30) REVERT: K 92 LYS cc_start: 0.8678 (tttm) cc_final: 0.8415 (tttm) REVERT: K 108 ARG cc_start: 0.3347 (mtt180) cc_final: 0.1062 (ptt90) REVERT: C 117 ASP cc_start: 0.8363 (p0) cc_final: 0.8032 (p0) REVERT: C 140 LYS cc_start: 0.8893 (tttt) cc_final: 0.8648 (ttmm) REVERT: C 229 GLU cc_start: 0.7719 (pp20) cc_final: 0.7425 (pp20) REVERT: C 235 GLU cc_start: 0.8192 (tt0) cc_final: 0.7578 (tm-30) REVERT: C 291 TRP cc_start: 0.6023 (p90) cc_final: 0.5383 (p90) REVERT: F 527 ILE cc_start: 0.5678 (mm) cc_final: 0.5136 (mm) REVERT: F 587 ARG cc_start: 0.8350 (mtp85) cc_final: 0.8032 (ttm-80) REVERT: I 36 TRP cc_start: 0.7658 (m100) cc_final: 0.6758 (m100) REVERT: I 38 ARG cc_start: 0.7881 (ttp-170) cc_final: 0.7456 (ptm160) REVERT: I 54 ASP cc_start: 0.8321 (p0) cc_final: 0.7805 (p0) REVERT: I 95 TYR cc_start: 0.7537 (m-80) cc_final: 0.7164 (m-10) REVERT: I 104 TYR cc_start: 0.8221 (m-10) cc_final: 0.7933 (m-10) REVERT: L 67 SER cc_start: 0.8018 (t) cc_final: 0.7750 (p) REVERT: L 81 GLU cc_start: 0.9152 (pm20) cc_final: 0.8884 (pm20) REVERT: L 104 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8203 (tt) REVERT: L 108 ARG cc_start: 0.3031 (mtt180) cc_final: 0.0760 (ptt90) outliers start: 22 outliers final: 14 residues processed: 390 average time/residue: 0.3131 time to fit residues: 166.8933 Evaluate side-chains 338 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 323 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN G 39 GLN J 37 GLN J 38 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN K 37 GLN K 38 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13998 Z= 0.368 Angle : 0.769 9.090 18999 Z= 0.381 Chirality : 0.049 0.194 2205 Planarity : 0.005 0.056 2370 Dihedral : 10.810 79.943 2451 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.53 % Allowed : 14.05 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -1.83 (0.20), residues: 1644 helix: 0.59 (0.40), residues: 180 sheet: -1.24 (0.20), residues: 639 loop : -1.54 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 36 HIS 0.003 0.001 HIS F 516 PHE 0.021 0.002 PHE L 71 TYR 0.023 0.002 TYR I 115 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 328 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7222 (mptt) REVERT: A 117 ASP cc_start: 0.8449 (p0) cc_final: 0.8108 (p0) REVERT: A 235 GLU cc_start: 0.8123 (tt0) cc_final: 0.7598 (tm-30) REVERT: D 587 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8072 (ttm110) REVERT: G 34 MET cc_start: 0.8315 (mmm) cc_final: 0.7908 (mmm) REVERT: G 54 ASP cc_start: 0.8337 (p0) cc_final: 0.8096 (p0) REVERT: G 57 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8118 (mmmm) REVERT: J 67 SER cc_start: 0.8257 (t) cc_final: 0.8045 (p) REVERT: J 70 ASP cc_start: 0.8574 (t70) cc_final: 0.8231 (t70) REVERT: J 90 GLN cc_start: 0.8672 (pp30) cc_final: 0.8093 (pp30) REVERT: J 92 LYS cc_start: 0.8764 (tttm) cc_final: 0.8461 (tttp) REVERT: J 104 LEU cc_start: 0.9003 (tp) cc_final: 0.8496 (tt) REVERT: J 108 ARG cc_start: 0.3356 (mtt180) cc_final: 0.1312 (ptt90) REVERT: B 56 LYS cc_start: 0.7384 (mmmt) cc_final: 0.7114 (mptt) REVERT: B 117 ASP cc_start: 0.8391 (p0) cc_final: 0.8035 (p0) REVERT: B 235 GLU cc_start: 0.8279 (tt0) cc_final: 0.7734 (tm-30) REVERT: E 587 ARG cc_start: 0.8407 (mtp85) cc_final: 0.7892 (ttm-80) REVERT: E 591 ASP cc_start: 0.8296 (t0) cc_final: 0.8022 (t0) REVERT: H 6 GLU cc_start: 0.5444 (mm-30) cc_final: 0.4906 (mm-30) REVERT: H 54 ASP cc_start: 0.8434 (p0) cc_final: 0.7904 (p0) REVERT: H 68 PHE cc_start: 0.5909 (m-80) cc_final: 0.5681 (m-80) REVERT: H 119 ASP cc_start: 0.8385 (p0) cc_final: 0.7927 (t70) REVERT: K 90 GLN cc_start: 0.8752 (pp30) cc_final: 0.8206 (pp30) REVERT: K 92 LYS cc_start: 0.8733 (tttm) cc_final: 0.7997 (ttmt) REVERT: K 108 ARG cc_start: 0.3342 (mtt180) cc_final: 0.1203 (ptt90) REVERT: C 56 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7133 (mptt) REVERT: C 117 ASP cc_start: 0.8373 (p0) cc_final: 0.8036 (p0) REVERT: C 229 GLU cc_start: 0.7780 (pp20) cc_final: 0.7425 (pp20) REVERT: C 235 GLU cc_start: 0.8244 (tt0) cc_final: 0.7550 (tm-30) REVERT: F 519 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9059 (p) REVERT: F 587 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7985 (ttm-80) REVERT: I 36 TRP cc_start: 0.7862 (m100) cc_final: 0.6386 (m100) REVERT: I 38 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7191 (ptm160) REVERT: I 54 ASP cc_start: 0.8319 (p0) cc_final: 0.7850 (p0) REVERT: I 57 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8475 (mmtp) REVERT: I 73 ASP cc_start: 0.8142 (t0) cc_final: 0.7928 (t0) REVERT: I 104 TYR cc_start: 0.8399 (m-10) cc_final: 0.8140 (m-10) REVERT: L 67 SER cc_start: 0.8032 (t) cc_final: 0.7554 (p) REVERT: L 104 LEU cc_start: 0.8904 (tp) cc_final: 0.8184 (tt) REVERT: L 108 ARG cc_start: 0.2942 (mtt180) cc_final: 0.0829 (ptt90) outliers start: 50 outliers final: 37 residues processed: 348 average time/residue: 0.2992 time to fit residues: 143.7090 Evaluate side-chains 336 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 298 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN L 31 ASN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13998 Z= 0.283 Angle : 0.699 8.775 18999 Z= 0.344 Chirality : 0.047 0.197 2205 Planarity : 0.004 0.048 2370 Dihedral : 9.386 77.478 2451 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.11 % Allowed : 15.47 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -1.61 (0.21), residues: 1644 helix: 0.97 (0.41), residues: 180 sheet: -1.13 (0.20), residues: 636 loop : -1.42 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.002 0.001 HIS G 35 PHE 0.012 0.002 PHE D 592 TYR 0.019 0.002 TYR G 115 ARG 0.004 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 318 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7603 (mmmt) cc_final: 0.7333 (mptt) REVERT: A 117 ASP cc_start: 0.8435 (p0) cc_final: 0.8134 (p0) REVERT: A 235 GLU cc_start: 0.8062 (tt0) cc_final: 0.7601 (tm-30) REVERT: D 587 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8181 (ttm-80) REVERT: G 34 MET cc_start: 0.8271 (mmm) cc_final: 0.7938 (mmm) REVERT: G 54 ASP cc_start: 0.8358 (p0) cc_final: 0.8100 (p0) REVERT: G 57 LYS cc_start: 0.8360 (mmmt) cc_final: 0.8148 (mmmm) REVERT: G 100 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7164 (mm) REVERT: J 18 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8010 (ttp80) REVERT: J 37 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: J 67 SER cc_start: 0.8339 (t) cc_final: 0.7870 (p) REVERT: J 90 GLN cc_start: 0.8744 (pp30) cc_final: 0.8120 (pp30) REVERT: J 92 LYS cc_start: 0.8808 (tttm) cc_final: 0.8545 (tttp) REVERT: J 104 LEU cc_start: 0.8920 (tp) cc_final: 0.8431 (tt) REVERT: J 108 ARG cc_start: 0.3217 (mtt180) cc_final: 0.1243 (ptt90) REVERT: B 89 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.6381 (tmt90) REVERT: B 117 ASP cc_start: 0.8382 (p0) cc_final: 0.7985 (p0) REVERT: B 235 GLU cc_start: 0.8248 (tt0) cc_final: 0.7751 (tm-30) REVERT: E 519 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.8989 (p) REVERT: E 587 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7816 (ttm-80) REVERT: E 588 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7652 (mmmm) REVERT: H 54 ASP cc_start: 0.8441 (p0) cc_final: 0.7969 (p0) REVERT: H 68 PHE cc_start: 0.6196 (m-80) cc_final: 0.5836 (m-80) REVERT: H 86 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7151 (mt) REVERT: H 119 ASP cc_start: 0.8344 (p0) cc_final: 0.8032 (t70) REVERT: K 90 GLN cc_start: 0.8777 (pp30) cc_final: 0.8193 (pp30) REVERT: K 108 ARG cc_start: 0.3344 (mtt180) cc_final: 0.1259 (ptt90) REVERT: C 56 LYS cc_start: 0.7638 (mmmt) cc_final: 0.7234 (mptt) REVERT: C 117 ASP cc_start: 0.8396 (p0) cc_final: 0.8058 (p0) REVERT: C 229 GLU cc_start: 0.7716 (pp20) cc_final: 0.7328 (pp20) REVERT: C 235 GLU cc_start: 0.8247 (tt0) cc_final: 0.7648 (tm-30) REVERT: F 587 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7963 (ttm-80) REVERT: I 38 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7358 (ptm160) REVERT: I 54 ASP cc_start: 0.8300 (p0) cc_final: 0.7815 (p0) REVERT: I 57 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8397 (mmtp) REVERT: I 73 ASP cc_start: 0.8186 (t0) cc_final: 0.7959 (t0) REVERT: I 83 MET cc_start: 0.7357 (mtm) cc_final: 0.6940 (mtm) REVERT: I 104 TYR cc_start: 0.8381 (m-10) cc_final: 0.8058 (m-10) REVERT: L 67 SER cc_start: 0.7972 (t) cc_final: 0.7693 (p) REVERT: L 104 LEU cc_start: 0.8854 (tp) cc_final: 0.8128 (tt) REVERT: L 108 ARG cc_start: 0.2958 (mtt180) cc_final: 0.0887 (ptt90) outliers start: 44 outliers final: 27 residues processed: 347 average time/residue: 0.2962 time to fit residues: 140.8149 Evaluate side-chains 329 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 297 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 118 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN C 39 HIS ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN I 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13998 Z= 0.161 Angle : 0.639 8.155 18999 Z= 0.314 Chirality : 0.045 0.196 2205 Planarity : 0.004 0.048 2370 Dihedral : 8.416 74.647 2451 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.26 % Allowed : 15.54 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -1.34 (0.21), residues: 1644 helix: 1.32 (0.41), residues: 180 sheet: -0.99 (0.20), residues: 633 loop : -1.25 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 36 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE F 582 TYR 0.015 0.001 TYR G 115 ARG 0.006 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 322 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7547 (mmmt) cc_final: 0.7329 (mptt) REVERT: A 117 ASP cc_start: 0.8420 (p0) cc_final: 0.8120 (p0) REVERT: A 235 GLU cc_start: 0.8018 (tt0) cc_final: 0.7525 (tm-30) REVERT: D 587 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8116 (ttm-80) REVERT: D 588 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7778 (mmmt) REVERT: G 5 GLU cc_start: 0.6775 (tp30) cc_final: 0.6546 (pm20) REVERT: G 34 MET cc_start: 0.8230 (mmm) cc_final: 0.7876 (mmm) REVERT: G 43 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7454 (mmmt) REVERT: G 46 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7793 (mm-30) REVERT: G 54 ASP cc_start: 0.8350 (p0) cc_final: 0.8091 (p0) REVERT: G 57 LYS cc_start: 0.8329 (mmmt) cc_final: 0.8115 (mmmm) REVERT: J 18 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8117 (ttp80) REVERT: J 37 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: J 58 VAL cc_start: 0.9158 (t) cc_final: 0.8926 (p) REVERT: J 61 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8141 (ptt180) REVERT: J 67 SER cc_start: 0.8294 (t) cc_final: 0.7846 (p) REVERT: J 71 PHE cc_start: 0.8590 (m-10) cc_final: 0.8302 (m-10) REVERT: J 90 GLN cc_start: 0.8761 (pp30) cc_final: 0.8180 (pp30) REVERT: J 92 LYS cc_start: 0.8827 (tttm) cc_final: 0.8505 (tttm) REVERT: J 103 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8574 (mtpp) REVERT: J 104 LEU cc_start: 0.8911 (tp) cc_final: 0.8379 (tt) REVERT: J 108 ARG cc_start: 0.3315 (mtt180) cc_final: 0.1304 (ptt90) REVERT: B 89 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6351 (tmt90) REVERT: B 117 ASP cc_start: 0.8314 (p0) cc_final: 0.7934 (p0) REVERT: B 235 GLU cc_start: 0.8238 (tt0) cc_final: 0.7767 (tm-30) REVERT: E 587 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7819 (ttm-80) REVERT: E 588 LYS cc_start: 0.8045 (mmmm) cc_final: 0.7779 (mmmm) REVERT: H 43 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7483 (mmmt) REVERT: H 54 ASP cc_start: 0.8411 (p0) cc_final: 0.7935 (p0) REVERT: H 119 ASP cc_start: 0.8296 (p0) cc_final: 0.8031 (t70) REVERT: K 90 GLN cc_start: 0.8805 (pp30) cc_final: 0.8199 (pp30) REVERT: K 108 ARG cc_start: 0.3043 (mtt180) cc_final: 0.1109 (ptt90) REVERT: C 56 LYS cc_start: 0.7531 (mmmt) cc_final: 0.7280 (mptt) REVERT: C 117 ASP cc_start: 0.8364 (p0) cc_final: 0.8058 (p0) REVERT: C 229 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7306 (pp20) REVERT: C 235 GLU cc_start: 0.8168 (tt0) cc_final: 0.7618 (tm-30) REVERT: C 291 TRP cc_start: 0.6006 (p90) cc_final: 0.5233 (p90) REVERT: F 587 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7969 (ttm-80) REVERT: I 38 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7526 (ptm160) REVERT: I 54 ASP cc_start: 0.8266 (p0) cc_final: 0.7807 (p0) REVERT: I 57 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8205 (mmtp) REVERT: I 73 ASP cc_start: 0.8108 (t0) cc_final: 0.7887 (t0) REVERT: I 83 MET cc_start: 0.7372 (mtm) cc_final: 0.6979 (mtm) REVERT: I 104 TYR cc_start: 0.8330 (m-10) cc_final: 0.8022 (m-10) REVERT: L 104 LEU cc_start: 0.8743 (tp) cc_final: 0.7989 (tt) REVERT: L 108 ARG cc_start: 0.2912 (mtt180) cc_final: 0.0902 (ptt90) outliers start: 32 outliers final: 20 residues processed: 339 average time/residue: 0.2991 time to fit residues: 139.1212 Evaluate side-chains 323 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 300 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN K 37 GLN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13998 Z= 0.250 Angle : 0.674 8.511 18999 Z= 0.331 Chirality : 0.046 0.195 2205 Planarity : 0.004 0.045 2370 Dihedral : 7.911 71.905 2451 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.97 % Allowed : 15.82 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -1.40 (0.21), residues: 1644 helix: 1.38 (0.40), residues: 183 sheet: -1.12 (0.20), residues: 654 loop : -1.23 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.002 0.001 HIS C 139 PHE 0.023 0.002 PHE I 50 TYR 0.016 0.001 TYR G 95 ARG 0.005 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 300 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7563 (mmmt) cc_final: 0.7344 (mptt) REVERT: A 117 ASP cc_start: 0.8401 (p0) cc_final: 0.8094 (p0) REVERT: A 235 GLU cc_start: 0.8063 (tt0) cc_final: 0.7585 (tm-30) REVERT: D 587 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8103 (ttm-80) REVERT: G 34 MET cc_start: 0.8190 (mmm) cc_final: 0.7851 (mmm) REVERT: G 43 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7625 (mmmt) REVERT: G 46 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7836 (mm-30) REVERT: G 54 ASP cc_start: 0.8403 (p0) cc_final: 0.8160 (p0) REVERT: G 57 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8071 (mmmm) REVERT: J 18 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8279 (ttp80) REVERT: J 37 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: J 58 VAL cc_start: 0.9108 (t) cc_final: 0.8863 (p) REVERT: J 61 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8154 (ptt180) REVERT: J 67 SER cc_start: 0.8275 (t) cc_final: 0.7737 (p) REVERT: J 90 GLN cc_start: 0.8785 (pp30) cc_final: 0.8319 (pp30) REVERT: J 92 LYS cc_start: 0.8867 (tttm) cc_final: 0.8553 (tttp) REVERT: J 104 LEU cc_start: 0.8872 (tp) cc_final: 0.8305 (tt) REVERT: J 108 ARG cc_start: 0.3252 (mtt180) cc_final: 0.1272 (ptt90) REVERT: B 56 LYS cc_start: 0.7144 (mptt) cc_final: 0.6814 (mmtt) REVERT: B 89 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.6298 (tmt90) REVERT: B 117 ASP cc_start: 0.8370 (p0) cc_final: 0.7982 (p0) REVERT: B 235 GLU cc_start: 0.8215 (tt0) cc_final: 0.7777 (tm-30) REVERT: E 519 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8986 (p) REVERT: E 587 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7810 (ttm-80) REVERT: H 43 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7530 (mmmt) REVERT: H 54 ASP cc_start: 0.8441 (p0) cc_final: 0.7977 (p0) REVERT: H 68 PHE cc_start: 0.6388 (m-80) cc_final: 0.5832 (m-80) REVERT: H 83 MET cc_start: 0.8313 (mmm) cc_final: 0.8032 (mmm) REVERT: K 67 SER cc_start: 0.8130 (t) cc_final: 0.7806 (p) REVERT: K 90 GLN cc_start: 0.8847 (pp30) cc_final: 0.8311 (pp30) REVERT: K 108 ARG cc_start: 0.2835 (mtt180) cc_final: 0.0890 (ptt90) REVERT: C 56 LYS cc_start: 0.7554 (mmmt) cc_final: 0.7306 (mptt) REVERT: C 117 ASP cc_start: 0.8411 (p0) cc_final: 0.8120 (p0) REVERT: C 229 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: C 235 GLU cc_start: 0.8208 (tt0) cc_final: 0.7634 (tm-30) REVERT: F 587 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7967 (ttm-80) REVERT: I 34 MET cc_start: 0.8200 (mmm) cc_final: 0.7926 (mmm) REVERT: I 38 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7466 (ptm160) REVERT: I 48 MET cc_start: 0.7037 (mmm) cc_final: 0.6775 (mmm) REVERT: I 54 ASP cc_start: 0.8363 (p0) cc_final: 0.7929 (p0) REVERT: I 73 ASP cc_start: 0.8119 (t0) cc_final: 0.7852 (t0) REVERT: I 104 TYR cc_start: 0.8485 (m-10) cc_final: 0.8253 (m-10) REVERT: L 67 SER cc_start: 0.8008 (t) cc_final: 0.7662 (p) REVERT: L 94 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7467 (t80) REVERT: L 104 LEU cc_start: 0.8789 (tp) cc_final: 0.7959 (tt) REVERT: L 108 ARG cc_start: 0.2933 (mtt180) cc_final: 0.0990 (ptt90) outliers start: 42 outliers final: 28 residues processed: 323 average time/residue: 0.2987 time to fit residues: 132.4587 Evaluate side-chains 324 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 0.0370 chunk 134 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN C 73 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13998 Z= 0.165 Angle : 0.640 8.196 18999 Z= 0.314 Chirality : 0.045 0.199 2205 Planarity : 0.004 0.046 2370 Dihedral : 7.499 69.036 2451 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.19 % Allowed : 16.17 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -1.19 (0.21), residues: 1644 helix: 1.59 (0.40), residues: 183 sheet: -0.96 (0.20), residues: 645 loop : -1.12 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 36 HIS 0.002 0.001 HIS G 35 PHE 0.026 0.002 PHE H 50 TYR 0.016 0.001 TYR G 115 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 311 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7577 (mmmt) cc_final: 0.7359 (mptt) REVERT: A 117 ASP cc_start: 0.8389 (p0) cc_final: 0.8122 (p0) REVERT: A 229 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7132 (pp20) REVERT: A 235 GLU cc_start: 0.8038 (tt0) cc_final: 0.7540 (tm-30) REVERT: D 587 ARG cc_start: 0.8315 (mtp85) cc_final: 0.8038 (ttm-80) REVERT: G 34 MET cc_start: 0.8157 (mmm) cc_final: 0.7774 (mmm) REVERT: G 46 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7867 (mm-30) REVERT: G 54 ASP cc_start: 0.8389 (p0) cc_final: 0.8134 (p0) REVERT: J 18 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8297 (ttp80) REVERT: J 37 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: J 58 VAL cc_start: 0.9169 (t) cc_final: 0.8927 (p) REVERT: J 61 ARG cc_start: 0.8518 (mtm180) cc_final: 0.8111 (ptt180) REVERT: J 67 SER cc_start: 0.8214 (t) cc_final: 0.7783 (p) REVERT: J 90 GLN cc_start: 0.8714 (pp30) cc_final: 0.8312 (pp30) REVERT: J 92 LYS cc_start: 0.8858 (tttm) cc_final: 0.8622 (tttm) REVERT: J 104 LEU cc_start: 0.8764 (tp) cc_final: 0.8162 (tt) REVERT: J 108 ARG cc_start: 0.3262 (mtt180) cc_final: 0.1327 (ptt90) REVERT: B 89 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6243 (tmt90) REVERT: B 117 ASP cc_start: 0.8348 (p0) cc_final: 0.7954 (p0) REVERT: B 235 GLU cc_start: 0.8187 (tt0) cc_final: 0.7765 (tm-30) REVERT: E 587 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7855 (ttm-80) REVERT: H 43 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7562 (mmmt) REVERT: H 54 ASP cc_start: 0.8390 (p0) cc_final: 0.7932 (p0) REVERT: K 67 SER cc_start: 0.8183 (t) cc_final: 0.7846 (p) REVERT: K 70 ASP cc_start: 0.8837 (t0) cc_final: 0.8357 (t0) REVERT: K 90 GLN cc_start: 0.8791 (pp30) cc_final: 0.8198 (pp30) REVERT: K 92 LYS cc_start: 0.8663 (tttm) cc_final: 0.8003 (ttmt) REVERT: K 94 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7349 (t80) REVERT: K 108 ARG cc_start: 0.2838 (mtt180) cc_final: 0.0947 (ptt90) REVERT: C 117 ASP cc_start: 0.8401 (p0) cc_final: 0.8128 (p0) REVERT: C 229 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7346 (pp20) REVERT: C 235 GLU cc_start: 0.8211 (tt0) cc_final: 0.7627 (tm-30) REVERT: F 587 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7929 (ttm-80) REVERT: I 34 MET cc_start: 0.8144 (mmm) cc_final: 0.7897 (mmm) REVERT: I 38 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7369 (ptm160) REVERT: I 54 ASP cc_start: 0.8345 (p0) cc_final: 0.7897 (p0) REVERT: I 57 LYS cc_start: 0.8936 (tptt) cc_final: 0.8331 (mmtp) REVERT: I 68 PHE cc_start: 0.6103 (m-80) cc_final: 0.5598 (m-10) REVERT: I 73 ASP cc_start: 0.8086 (t0) cc_final: 0.7815 (t0) REVERT: I 104 TYR cc_start: 0.8422 (m-10) cc_final: 0.8197 (m-10) REVERT: L 67 SER cc_start: 0.8014 (t) cc_final: 0.7633 (p) REVERT: L 94 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7570 (t80) REVERT: L 104 LEU cc_start: 0.8734 (tp) cc_final: 0.7901 (tt) REVERT: L 108 ARG cc_start: 0.2908 (mtt180) cc_final: 0.0995 (ptt90) outliers start: 31 outliers final: 20 residues processed: 326 average time/residue: 0.3074 time to fit residues: 137.6256 Evaluate side-chains 316 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 290 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.0370 chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN K 37 GLN C 73 ASN ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13998 Z= 0.243 Angle : 0.673 8.579 18999 Z= 0.330 Chirality : 0.046 0.179 2205 Planarity : 0.004 0.048 2370 Dihedral : 7.322 66.912 2451 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.75 % Allowed : 16.74 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: -1.27 (0.21), residues: 1644 helix: 1.65 (0.40), residues: 183 sheet: -1.02 (0.20), residues: 648 loop : -1.20 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.002 0.001 HIS G 35 PHE 0.023 0.002 PHE E 592 TYR 0.017 0.001 TYR G 115 ARG 0.004 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 289 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8362 (p0) cc_final: 0.8070 (p0) REVERT: A 229 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: A 235 GLU cc_start: 0.8070 (tt0) cc_final: 0.7541 (tm-30) REVERT: D 587 ARG cc_start: 0.8335 (mtp85) cc_final: 0.8066 (ttm-80) REVERT: G 34 MET cc_start: 0.8103 (mmm) cc_final: 0.7773 (mmm) REVERT: G 46 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7901 (mm-30) REVERT: G 54 ASP cc_start: 0.8341 (p0) cc_final: 0.8097 (p0) REVERT: J 18 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8359 (ttp80) REVERT: J 37 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: J 58 VAL cc_start: 0.9173 (t) cc_final: 0.8958 (p) REVERT: J 61 ARG cc_start: 0.8533 (mtm180) cc_final: 0.8132 (ptt180) REVERT: J 67 SER cc_start: 0.8105 (t) cc_final: 0.7770 (p) REVERT: J 90 GLN cc_start: 0.8697 (pp30) cc_final: 0.8330 (pp30) REVERT: J 92 LYS cc_start: 0.9020 (tttm) cc_final: 0.8758 (tttm) REVERT: J 104 LEU cc_start: 0.8738 (tp) cc_final: 0.8136 (tt) REVERT: J 108 ARG cc_start: 0.3235 (mtt180) cc_final: 0.1326 (ptt90) REVERT: B 56 LYS cc_start: 0.7301 (mptt) cc_final: 0.6975 (mmtt) REVERT: B 89 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.6245 (tmt90) REVERT: B 117 ASP cc_start: 0.8373 (p0) cc_final: 0.7985 (p0) REVERT: B 235 GLU cc_start: 0.8243 (tt0) cc_final: 0.7784 (tm-30) REVERT: E 519 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8989 (p) REVERT: E 587 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7785 (ttm-80) REVERT: H 43 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7621 (mmmt) REVERT: H 54 ASP cc_start: 0.8408 (p0) cc_final: 0.7982 (p0) REVERT: K 67 SER cc_start: 0.8165 (t) cc_final: 0.7772 (p) REVERT: K 90 GLN cc_start: 0.8792 (pp30) cc_final: 0.8263 (pp30) REVERT: K 94 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7544 (t80) REVERT: K 108 ARG cc_start: 0.2820 (mtt180) cc_final: 0.0909 (ptt90) REVERT: C 56 LYS cc_start: 0.7423 (mptt) cc_final: 0.7204 (mptt) REVERT: C 117 ASP cc_start: 0.8379 (p0) cc_final: 0.8116 (p0) REVERT: C 229 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7500 (pp20) REVERT: C 235 GLU cc_start: 0.8235 (tt0) cc_final: 0.7632 (tm-30) REVERT: F 519 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9100 (p) REVERT: F 587 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7958 (ttm-80) REVERT: I 34 MET cc_start: 0.8142 (mmm) cc_final: 0.7915 (mmm) REVERT: I 38 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7475 (ptm160) REVERT: I 54 ASP cc_start: 0.8320 (p0) cc_final: 0.7879 (p0) REVERT: I 73 ASP cc_start: 0.8096 (t0) cc_final: 0.7777 (t0) REVERT: I 104 TYR cc_start: 0.8442 (m-10) cc_final: 0.8191 (m-10) REVERT: L 67 SER cc_start: 0.7918 (t) cc_final: 0.7525 (p) REVERT: L 92 LYS cc_start: 0.8783 (tttm) cc_final: 0.8095 (ttmt) REVERT: L 94 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7605 (t80) REVERT: L 104 LEU cc_start: 0.8698 (tp) cc_final: 0.7838 (tt) REVERT: L 108 ARG cc_start: 0.2824 (mtt180) cc_final: 0.0944 (ptt90) outliers start: 39 outliers final: 27 residues processed: 310 average time/residue: 0.3092 time to fit residues: 131.2514 Evaluate side-chains 317 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 282 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 94 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.7848 > 50: distance: 23 - 30: 4.130 distance: 30 - 31: 5.588 distance: 31 - 32: 13.473 distance: 31 - 34: 11.817 distance: 32 - 33: 16.942 distance: 32 - 36: 8.251 distance: 34 - 35: 21.845 distance: 35 - 109: 19.067 distance: 36 - 37: 25.602 distance: 37 - 38: 50.647 distance: 37 - 40: 45.375 distance: 38 - 39: 23.598 distance: 38 - 44: 22.953 distance: 40 - 41: 13.520 distance: 41 - 42: 17.581 distance: 41 - 43: 27.254 distance: 44 - 45: 16.582 distance: 44 - 50: 12.809 distance: 45 - 46: 35.014 distance: 45 - 48: 24.780 distance: 46 - 47: 12.915 distance: 46 - 51: 26.189 distance: 48 - 49: 6.855 distance: 49 - 50: 30.029 distance: 51 - 52: 15.422 distance: 52 - 53: 22.766 distance: 52 - 55: 8.752 distance: 53 - 54: 17.324 distance: 53 - 56: 18.293 distance: 56 - 57: 13.403 distance: 57 - 58: 21.934 distance: 57 - 60: 4.136 distance: 58 - 59: 10.047 distance: 58 - 61: 19.398 distance: 61 - 62: 20.089 distance: 61 - 67: 20.754 distance: 62 - 63: 15.537 distance: 62 - 65: 24.202 distance: 63 - 64: 12.434 distance: 63 - 68: 11.690 distance: 65 - 66: 37.788 distance: 66 - 67: 25.932 distance: 68 - 69: 18.890 distance: 69 - 70: 28.044 distance: 69 - 72: 28.022 distance: 70 - 71: 24.642 distance: 70 - 76: 28.769 distance: 72 - 73: 6.339 distance: 73 - 74: 16.142 distance: 73 - 75: 39.511 distance: 76 - 77: 25.713 distance: 77 - 78: 16.143 distance: 78 - 79: 12.925 distance: 78 - 80: 11.840 distance: 80 - 81: 7.708 distance: 81 - 82: 12.898 distance: 81 - 84: 10.555 distance: 82 - 83: 11.882 distance: 82 - 88: 6.366 distance: 84 - 85: 21.281 distance: 84 - 86: 21.459 distance: 85 - 87: 17.172 distance: 88 - 89: 8.191 distance: 89 - 90: 11.286 distance: 89 - 92: 12.160 distance: 90 - 91: 12.368 distance: 90 - 99: 11.055 distance: 92 - 93: 12.137 distance: 93 - 94: 5.857 distance: 94 - 95: 4.074 distance: 95 - 96: 3.675 distance: 96 - 97: 5.320 distance: 96 - 98: 5.271