Starting phenix.real_space_refine on Fri Feb 16 23:04:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/02_2024/6mlm_9139.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/02_2024/6mlm_9139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/02_2024/6mlm_9139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/02_2024/6mlm_9139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/02_2024/6mlm_9139.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/02_2024/6mlm_9139.pdb" } resolution = 3.5 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= 0.008 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 90 5.16 5 C 10416 2.51 5 N 2895 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16701 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "C" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1369 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "I" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1369 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2399 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "J" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1369 Classifications: {'peptide': 168} Link IDs: {'TRANS': 167} Chain: "K" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" 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: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.91, per 1000 atoms: 0.53 Number of scatterers: 16701 At special positions: 0 Unit cell: (116.28, 113.22, 167.28, 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 90 16.00 O 3300 8.00 N 2895 7.00 C 10416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS C 137 " distance=2.07 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 293 " distance=2.16 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 321 " distance=2.07 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS D 137 " distance=2.07 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 293 " distance=2.16 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 321 " distance=2.07 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 30 " - pdb=" SG CYS J 137 " distance=2.07 Simple disulfide: pdb=" SG CYS H 68 " - pdb=" SG CYS H 293 " distance=2.16 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 155 " distance=2.03 Simple disulfide: pdb=" SG CYS H 297 " - pdb=" SG CYS H 321 " distance=2.07 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 148 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 54 " " NAG A 802 " - " ASN A 256 " " NAG B 801 " - " ASN B 54 " " NAG B 802 " - " ASN B 256 " " NAG C 301 " - " ASN C 82 " " NAG D 301 " - " ASN D 82 " " NAG H 801 " - " ASN H 54 " " NAG H 802 " - " ASN H 256 " " NAG J 301 " - " ASN J 82 " Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 3.1 seconds 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3858 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 54 sheets defined 21.5% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.617A pdb=" N ASP A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 96 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'C' and resid 37 through 49 removed outlier: 4.162A pdb=" N THR C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 57 Processing helix chain 'C' and resid 74 through 127 Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.539A pdb=" N MET C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 removed outlier: 4.868A pdb=" N THR C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.616A pdb=" N ASP B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLN B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 96 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'D' and resid 37 through 49 removed outlier: 4.162A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.539A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 171 removed outlier: 4.869A pdb=" N THR D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 89 through 96 removed outlier: 3.616A pdb=" N ASP H 93 " --> pdb=" O PRO H 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN H 94 " --> pdb=" O GLN H 91 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU H 96 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 130 Processing helix chain 'H' and resid 155 through 160 Processing helix chain 'H' and resid 203 through 212 Processing helix chain 'J' and resid 37 through 49 removed outlier: 4.163A pdb=" N THR J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 57 Processing helix chain 'J' and resid 74 through 127 Processing helix chain 'J' and resid 145 through 154 removed outlier: 3.539A pdb=" N MET J 149 " --> pdb=" O ASP J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 171 removed outlier: 4.868A pdb=" N THR J 164 " --> pdb=" O THR J 160 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN J 169 " --> pdb=" O GLU J 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.104A pdb=" N ASP A 27 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 removed outlier: 3.754A pdb=" N THR A 40 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.018A pdb=" N ILE A 67 " --> pdb=" O ASP A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.414A pdb=" N THR A 75 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.553A pdb=" N ARG A 117 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N TRP A 250 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE A 195 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 180 through 185 Processing sheet with id=AB1, first strand: chain 'A' and resid 297 through 299 removed outlier: 4.081A pdb=" N CYS A 297 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.824A pdb=" N PHE E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE E 50 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'E' and resid 18 through 20 Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.121A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.121A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.104A pdb=" N ASP B 27 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 40 through 43 removed outlier: 3.755A pdb=" N THR B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AC4, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AC5, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.017A pdb=" N ILE B 67 " --> pdb=" O ASP B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.414A pdb=" N THR B 75 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.553A pdb=" N ARG B 117 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N TRP B 250 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE B 195 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 180 through 185 Processing sheet with id=AD1, first strand: chain 'B' and resid 297 through 299 removed outlier: 4.081A pdb=" N CYS B 297 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 319 through 321 Processing sheet with id=AD3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.823A pdb=" N PHE F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'F' and resid 18 through 20 Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 24 through 27 removed outlier: 4.104A pdb=" N ASP H 27 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 40 through 43 removed outlier: 3.754A pdb=" N THR H 40 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 55 through 57 Processing sheet with id=AE4, first strand: chain 'H' and resid 59 through 60 Processing sheet with id=AE5, first strand: chain 'H' and resid 67 through 68 removed outlier: 6.018A pdb=" N ILE H 67 " --> pdb=" O ASP H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'H' and resid 75 through 76 removed outlier: 6.414A pdb=" N THR H 75 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AE8, first strand: chain 'H' and resid 116 through 118 removed outlier: 6.554A pdb=" N ARG H 117 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N TRP H 250 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE H 195 " --> pdb=" O PRO H 270 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 180 through 185 Processing sheet with id=AF1, first strand: chain 'H' and resid 297 through 299 removed outlier: 4.080A pdb=" N CYS H 297 " --> pdb=" O ILE H 304 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 319 through 321 Processing sheet with id=AF3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.824A pdb=" N PHE K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'K' and resid 18 through 20 Processing sheet with id=AF7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.120A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.120A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1737 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: 5.66 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4627 1.33 - 1.46: 4753 1.46 - 1.59: 7537 1.59 - 1.72: 0 1.72 - 1.85: 132 Bond restraints: 17049 Sorted by residual: bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" C1 NAG H 802 " pdb=" O5 NAG H 802 " ideal model delta sigma weight residual 1.406 1.550 -0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C1 NAG B 802 " pdb=" O5 NAG B 802 " ideal model delta sigma weight residual 1.406 1.550 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C1 NAG D 301 " pdb=" O5 NAG D 301 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C1 NAG C 301 " pdb=" O5 NAG C 301 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 17044 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.49: 397 105.49 - 112.59: 8344 112.59 - 119.68: 5483 119.68 - 126.77: 8668 126.77 - 133.86: 169 Bond angle restraints: 23061 Sorted by residual: angle pdb=" C GLY A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta sigma weight residual 119.66 126.35 -6.69 7.30e-01 1.88e+00 8.40e+01 angle pdb=" C GLY H 88 " pdb=" N PRO H 89 " pdb=" CA PRO H 89 " ideal model delta sigma weight residual 119.66 126.33 -6.67 7.30e-01 1.88e+00 8.35e+01 angle pdb=" C GLY B 88 " pdb=" N PRO B 89 " pdb=" CA PRO B 89 " ideal model delta sigma weight residual 119.66 126.32 -6.66 7.30e-01 1.88e+00 8.32e+01 angle pdb=" C LEU H 308 " pdb=" N PRO H 309 " pdb=" CA PRO H 309 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.01e+00 9.80e-01 6.87e+01 angle pdb=" C LEU B 308 " pdb=" N PRO B 309 " pdb=" CA PRO B 309 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.01e+00 9.80e-01 6.87e+01 ... (remaining 23056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 9869 17.65 - 35.30: 316 35.30 - 52.96: 69 52.96 - 70.61: 57 70.61 - 88.26: 21 Dihedral angle restraints: 10332 sinusoidal: 4284 harmonic: 6048 Sorted by residual: dihedral pdb=" CB CYS H 297 " pdb=" SG CYS H 297 " pdb=" SG CYS H 321 " pdb=" CB CYS H 321 " ideal model delta sinusoidal sigma weight residual -86.00 -148.66 62.66 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS B 297 " pdb=" SG CYS B 297 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual -86.00 -148.66 62.66 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS A 297 " pdb=" SG CYS A 297 " pdb=" SG CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sinusoidal sigma weight residual -86.00 -148.65 62.65 1 1.00e+01 1.00e-02 5.19e+01 ... (remaining 10329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1778 0.055 - 0.110: 579 0.110 - 0.164: 133 0.164 - 0.219: 21 0.219 - 0.274: 6 Chirality restraints: 2517 Sorted by residual: chirality pdb=" CA CYS H 297 " pdb=" N CYS H 297 " pdb=" C CYS H 297 " pdb=" CB CYS H 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA CYS B 297 " pdb=" N CYS B 297 " pdb=" C CYS B 297 " pdb=" CB CYS B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA CYS A 297 " pdb=" N CYS A 297 " pdb=" C CYS A 297 " pdb=" CB CYS A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2514 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 54 " -0.109 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN A 54 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 54 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 54 " 0.185 2.00e-02 2.50e+03 pdb=" C1 NAG A 801 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 54 " -0.109 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN B 54 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 54 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 54 " 0.185 2.00e-02 2.50e+03 pdb=" C1 NAG B 801 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 54 " -0.108 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN H 54 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN H 54 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN H 54 " 0.185 2.00e-02 2.50e+03 pdb=" C1 NAG H 801 " -0.146 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4528 2.80 - 3.33: 15042 3.33 - 3.85: 28138 3.85 - 4.38: 33103 4.38 - 4.90: 56559 Nonbonded interactions: 137370 Sorted by model distance: nonbonded pdb=" O ASP J 174 " pdb=" OD1 ASP J 174 " model vdw 2.276 3.040 nonbonded pdb=" O ASP C 174 " pdb=" OD1 ASP C 174 " model vdw 2.277 3.040 nonbonded pdb=" O ASP D 174 " pdb=" OD1 ASP D 174 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR K 99 " pdb=" OD1 ASN L 34 " model vdw 2.372 2.440 nonbonded pdb=" OH TYR F 99 " pdb=" OD1 ASN G 34 " model vdw 2.372 2.440 ... (remaining 137365 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 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'L' } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.590 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 46.220 Find NCS groups from input model: 1.040 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.013 0.145 17049 Z= 0.871 Angle : 1.310 9.731 23061 Z= 0.889 Chirality : 0.057 0.274 2517 Planarity : 0.005 0.022 3009 Dihedral : 11.419 88.259 6402 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.00 % Favored : 96.71 % Rotamer: Outliers : 0.33 % Allowed : 0.66 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2097 helix: 1.13 (0.25), residues: 336 sheet: 0.44 (0.21), residues: 537 loop : -0.01 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP I 35 HIS 0.005 0.001 HIS K 35 PHE 0.024 0.003 PHE D 24 TYR 0.029 0.004 TYR C 157 ARG 0.002 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 504 time to evaluate : 1.951 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 69 THR cc_start: 0.6336 (p) cc_final: 0.5437 (m) REVERT: C 21 TRP cc_start: 0.5789 (m-10) cc_final: 0.5275 (m-10) REVERT: C 120 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8107 (tm-30) REVERT: C 133 ASP cc_start: 0.4360 (m-30) cc_final: 0.4137 (m-30) REVERT: B 41 LYS cc_start: 0.7949 (mttt) cc_final: 0.7650 (mtmm) REVERT: B 69 THR cc_start: 0.6655 (p) cc_final: 0.6038 (m) REVERT: D 21 TRP cc_start: 0.6041 (m-10) cc_final: 0.5540 (m-10) REVERT: D 120 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8154 (tm-30) REVERT: D 132 GLU cc_start: 0.4127 (tt0) cc_final: 0.3753 (pm20) REVERT: D 133 ASP cc_start: 0.4285 (m-30) cc_final: 0.4049 (m-30) REVERT: G 104 LEU cc_start: 0.8373 (mp) cc_final: 0.8118 (mt) REVERT: H 51 GLU cc_start: 0.7793 (tt0) cc_final: 0.7581 (tp30) REVERT: H 69 THR cc_start: 0.6761 (p) cc_final: 0.5832 (m) REVERT: J 21 TRP cc_start: 0.6110 (m-10) cc_final: 0.5727 (m-10) REVERT: J 120 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8133 (tm-30) REVERT: J 132 GLU cc_start: 0.4032 (tt0) cc_final: 0.3674 (pm20) REVERT: J 152 ILE cc_start: 0.6309 (mt) cc_final: 0.6049 (mt) REVERT: L 55 GLN cc_start: 0.6402 (tp-100) cc_final: 0.6177 (tt0) REVERT: L 104 LEU cc_start: 0.8322 (mp) cc_final: 0.8118 (mt) outliers start: 6 outliers final: 1 residues processed: 509 average time/residue: 0.3522 time to fit residues: 249.9576 Evaluate side-chains 261 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 312 ASN B 126 GLN B 179 GLN B 327 GLN B 338 ASN D 42 GLN D 106 HIS F 3 GLN H 179 GLN H 312 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17049 Z= 0.229 Angle : 0.706 10.981 23061 Z= 0.373 Chirality : 0.045 0.234 2517 Planarity : 0.004 0.044 3009 Dihedral : 6.453 65.744 2495 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.58 % Allowed : 7.74 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2097 helix: 1.12 (0.26), residues: 327 sheet: 0.75 (0.21), residues: 576 loop : -0.52 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 14 HIS 0.005 0.001 HIS C 142 PHE 0.026 0.002 PHE D 138 TYR 0.020 0.002 TYR D 119 ARG 0.010 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 304 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.6187 (p) cc_final: 0.5266 (p) REVERT: C 149 MET cc_start: 0.4412 (tpt) cc_final: 0.3436 (ptt) REVERT: B 69 THR cc_start: 0.6578 (p) cc_final: 0.6223 (p) REVERT: D 22 TYR cc_start: 0.7687 (m-80) cc_final: 0.7338 (m-80) REVERT: D 61 GLN cc_start: 0.5769 (OUTLIER) cc_final: 0.5517 (mm110) REVERT: D 149 MET cc_start: 0.4320 (tpt) cc_final: 0.3537 (ptt) REVERT: F 94 ARG cc_start: 0.7898 (tmm-80) cc_final: 0.7286 (ttm170) REVERT: H 69 THR cc_start: 0.6553 (p) cc_final: 0.5676 (p) REVERT: J 21 TRP cc_start: 0.5384 (m-10) cc_final: 0.5180 (m-10) REVERT: J 149 MET cc_start: 0.4724 (tpt) cc_final: 0.3920 (ptt) REVERT: K 48 MET cc_start: 0.7616 (mtm) cc_final: 0.7399 (mtm) outliers start: 47 outliers final: 22 residues processed: 327 average time/residue: 0.3033 time to fit residues: 147.3346 Evaluate side-chains 257 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 203 optimal weight: 0.0040 chunk 167 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17049 Z= 0.372 Angle : 0.723 10.027 23061 Z= 0.381 Chirality : 0.045 0.198 2517 Planarity : 0.005 0.041 3009 Dihedral : 6.280 59.924 2495 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.68 % Allowed : 9.88 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2097 helix: 0.97 (0.27), residues: 318 sheet: 0.57 (0.21), residues: 513 loop : -0.94 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 21 HIS 0.006 0.002 HIS E 35 PHE 0.027 0.002 PHE L 71 TYR 0.018 0.002 TYR H 143 ARG 0.005 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 239 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 TRP cc_start: 0.5771 (m-10) cc_final: 0.5556 (m-10) REVERT: C 22 TYR cc_start: 0.7840 (m-80) cc_final: 0.7391 (m-80) REVERT: C 103 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8599 (mp0) REVERT: C 149 MET cc_start: 0.4544 (tpt) cc_final: 0.4276 (tpt) REVERT: I 50 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: D 22 TYR cc_start: 0.7396 (m-80) cc_final: 0.7108 (m-80) REVERT: D 149 MET cc_start: 0.4250 (tpt) cc_final: 0.3753 (ppp) REVERT: F 81 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: G 70 GLU cc_start: 0.5486 (tm-30) cc_final: 0.5216 (pp20) REVERT: H 51 GLU cc_start: 0.7426 (tp30) cc_final: 0.7040 (tp30) REVERT: J 21 TRP cc_start: 0.5117 (m-10) cc_final: 0.4746 (m-10) outliers start: 67 outliers final: 40 residues processed: 271 average time/residue: 0.2656 time to fit residues: 111.8044 Evaluate side-chains 261 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17049 Z= 0.215 Angle : 0.623 9.012 23061 Z= 0.324 Chirality : 0.042 0.226 2517 Planarity : 0.004 0.039 3009 Dihedral : 5.746 43.034 2493 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.13 % Allowed : 12.69 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2097 helix: 0.97 (0.27), residues: 318 sheet: 0.49 (0.22), residues: 477 loop : -0.97 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 47 HIS 0.004 0.001 HIS E 35 PHE 0.034 0.002 PHE L 71 TYR 0.015 0.001 TYR D 157 ARG 0.013 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 234 time to evaluate : 1.785 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: C 22 TYR cc_start: 0.7703 (m-80) cc_final: 0.7476 (m-80) REVERT: C 103 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8541 (mp0) REVERT: C 149 MET cc_start: 0.4414 (tpt) cc_final: 0.4119 (tpt) REVERT: I 50 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: D 22 TYR cc_start: 0.7579 (m-80) cc_final: 0.7235 (m-80) REVERT: F 69 MET cc_start: 0.7574 (mtp) cc_final: 0.7280 (mtp) REVERT: G 70 GLU cc_start: 0.5608 (tm-30) cc_final: 0.5306 (pp20) REVERT: G 105 GLU cc_start: 0.6933 (mp0) cc_final: 0.6679 (mp0) REVERT: J 149 MET cc_start: 0.3782 (tpt) cc_final: 0.2646 (ptt) outliers start: 57 outliers final: 38 residues processed: 259 average time/residue: 0.2795 time to fit residues: 110.9409 Evaluate side-chains 257 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.6980 chunk 113 optimal weight: 0.0980 chunk 2 optimal weight: 0.0060 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 102 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17049 Z= 0.257 Angle : 0.630 8.784 23061 Z= 0.328 Chirality : 0.042 0.220 2517 Planarity : 0.004 0.057 3009 Dihedral : 5.679 36.424 2493 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.57 % Allowed : 13.29 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2097 helix: 0.88 (0.27), residues: 318 sheet: 0.25 (0.22), residues: 477 loop : -1.07 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 21 HIS 0.005 0.001 HIS C 142 PHE 0.015 0.002 PHE H 298 TYR 0.016 0.002 TYR J 22 ARG 0.012 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 223 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 TRP cc_start: 0.5666 (m-10) cc_final: 0.5268 (m-10) REVERT: C 149 MET cc_start: 0.4350 (tpt) cc_final: 0.3581 (ppp) REVERT: I 50 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: D 102 MET cc_start: 0.8596 (mtp) cc_final: 0.8334 (mtp) REVERT: D 103 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8518 (mp0) REVERT: D 120 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7888 (pp20) REVERT: G 70 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5631 (pp20) REVERT: J 102 MET cc_start: 0.8298 (mtp) cc_final: 0.8062 (mtp) REVERT: J 149 MET cc_start: 0.3781 (tpt) cc_final: 0.2619 (ptt) REVERT: K 38 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7967 (mtp180) outliers start: 65 outliers final: 46 residues processed: 253 average time/residue: 0.2663 time to fit residues: 103.8652 Evaluate side-chains 260 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 66 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17049 Z= 0.242 Angle : 0.610 8.880 23061 Z= 0.317 Chirality : 0.042 0.204 2517 Planarity : 0.004 0.046 3009 Dihedral : 5.533 31.108 2493 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.12 % Allowed : 13.01 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2097 helix: 1.04 (0.27), residues: 318 sheet: 0.35 (0.23), residues: 447 loop : -1.14 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 21 HIS 0.004 0.001 HIS D 142 PHE 0.018 0.002 PHE A 298 TYR 0.021 0.002 TYR J 22 ARG 0.014 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 223 time to evaluate : 1.868 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: C 21 TRP cc_start: 0.5691 (m-10) cc_final: 0.5448 (m-10) REVERT: E 38 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7641 (mtm110) REVERT: I 50 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: D 120 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7941 (pp20) REVERT: F 69 MET cc_start: 0.7719 (mtp) cc_final: 0.7473 (mtp) REVERT: G 70 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5620 (pp20) REVERT: G 100 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6698 (pt0) REVERT: G 105 GLU cc_start: 0.7080 (mp0) cc_final: 0.6867 (mp0) REVERT: J 149 MET cc_start: 0.3951 (tpt) cc_final: 0.2766 (ptt) outliers start: 75 outliers final: 53 residues processed: 263 average time/residue: 0.2712 time to fit residues: 108.7298 Evaluate side-chains 271 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 215 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17049 Z= 0.224 Angle : 0.598 8.434 23061 Z= 0.311 Chirality : 0.042 0.224 2517 Planarity : 0.004 0.041 3009 Dihedral : 5.418 28.428 2493 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.90 % Allowed : 13.95 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2097 helix: 1.16 (0.27), residues: 318 sheet: 0.26 (0.23), residues: 453 loop : -1.18 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 21 HIS 0.005 0.001 HIS J 142 PHE 0.017 0.002 PHE A 298 TYR 0.022 0.001 TYR C 157 ARG 0.009 0.000 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 223 time to evaluate : 1.964 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: C 21 TRP cc_start: 0.5799 (m-10) cc_final: 0.5593 (m-10) REVERT: I 50 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: I 105 GLU cc_start: 0.7052 (mp0) cc_final: 0.6783 (mp0) REVERT: D 120 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7993 (pp20) REVERT: G 100 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6696 (pt0) REVERT: H 30 CYS cc_start: 0.2643 (m) cc_final: 0.2439 (m) REVERT: H 217 LEU cc_start: 0.8557 (tt) cc_final: 0.8298 (tp) REVERT: J 149 MET cc_start: 0.3951 (tpt) cc_final: 0.2761 (ptt) outliers start: 71 outliers final: 54 residues processed: 265 average time/residue: 0.2738 time to fit residues: 111.0990 Evaluate side-chains 268 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 212 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17049 Z= 0.317 Angle : 0.656 8.987 23061 Z= 0.343 Chirality : 0.043 0.237 2517 Planarity : 0.004 0.047 3009 Dihedral : 5.664 28.961 2493 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.12 % Allowed : 14.17 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2097 helix: 1.13 (0.28), residues: 315 sheet: 0.11 (0.23), residues: 453 loop : -1.28 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 21 HIS 0.006 0.001 HIS J 142 PHE 0.020 0.002 PHE L 71 TYR 0.021 0.002 TYR D 157 ARG 0.011 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 214 time to evaluate : 1.889 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 130 ARG cc_start: 0.7230 (ptt90) cc_final: 0.6999 (ptt-90) REVERT: A 202 GLU cc_start: 0.7343 (tp30) cc_final: 0.7100 (tp30) REVERT: C 21 TRP cc_start: 0.6053 (m-10) cc_final: 0.5743 (m-10) REVERT: E 38 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7813 (mtm110) REVERT: D 120 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8016 (pp20) REVERT: G 70 GLU cc_start: 0.6180 (tm-30) cc_final: 0.5956 (tm-30) REVERT: G 100 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6741 (pt0) REVERT: H 139 MET cc_start: 0.7574 (ttm) cc_final: 0.7366 (ttm) REVERT: H 217 LEU cc_start: 0.8587 (tt) cc_final: 0.8355 (tp) REVERT: J 149 MET cc_start: 0.3849 (tpt) cc_final: 0.2673 (ptt) outliers start: 75 outliers final: 62 residues processed: 259 average time/residue: 0.2716 time to fit residues: 107.2487 Evaluate side-chains 269 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 206 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 263 PHE Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 185 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17049 Z= 0.375 Angle : 0.693 9.189 23061 Z= 0.362 Chirality : 0.044 0.218 2517 Planarity : 0.005 0.052 3009 Dihedral : 5.985 34.179 2493 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.68 % Allowed : 15.16 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2097 helix: 1.02 (0.28), residues: 315 sheet: -0.33 (0.22), residues: 504 loop : -1.44 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 21 HIS 0.007 0.001 HIS J 142 PHE 0.020 0.002 PHE A 163 TYR 0.020 0.002 TYR D 157 ARG 0.015 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 216 time to evaluate : 2.075 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: A 130 ARG cc_start: 0.7322 (ptt90) cc_final: 0.7094 (ptt-90) REVERT: D 120 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7972 (pp20) REVERT: G 100 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6842 (pt0) REVERT: J 149 MET cc_start: 0.3854 (tpt) cc_final: 0.2952 (mmm) outliers start: 67 outliers final: 58 residues processed: 261 average time/residue: 0.2678 time to fit residues: 107.6006 Evaluate side-chains 266 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 207 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 263 PHE Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain L residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 0.0070 chunk 100 optimal weight: 0.0020 chunk 130 optimal weight: 0.8980 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17049 Z= 0.169 Angle : 0.603 9.312 23061 Z= 0.313 Chirality : 0.042 0.203 2517 Planarity : 0.004 0.046 3009 Dihedral : 5.309 28.030 2493 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.31 % Allowed : 16.86 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2097 helix: 1.35 (0.28), residues: 315 sheet: -0.18 (0.22), residues: 501 loop : -1.25 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 21 HIS 0.006 0.001 HIS D 142 PHE 0.017 0.001 PHE C 138 TYR 0.024 0.001 TYR D 157 ARG 0.014 0.001 ARG C 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 TRP cc_start: 0.6239 (m-10) cc_final: 0.5913 (m-10) REVERT: D 120 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8006 (pp20) REVERT: G 70 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5876 (tm-30) REVERT: H 112 ILE cc_start: 0.8562 (pp) cc_final: 0.8311 (pt) REVERT: H 217 LEU cc_start: 0.8466 (tt) cc_final: 0.8264 (tp) REVERT: J 149 MET cc_start: 0.3984 (tpt) cc_final: 0.2778 (ptt) outliers start: 42 outliers final: 34 residues processed: 254 average time/residue: 0.2855 time to fit residues: 108.6655 Evaluate side-chains 241 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 263 PHE Chi-restraints excluded: chain H residue 291 SER Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 105 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 144 optimal weight: 0.0670 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN B 149 ASN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.149865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124798 restraints weight = 37104.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125665 restraints weight = 23923.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126478 restraints weight = 18894.716| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17049 Z= 0.246 Angle : 0.645 8.579 23061 Z= 0.337 Chirality : 0.044 0.374 2517 Planarity : 0.005 0.070 3009 Dihedral : 5.399 28.598 2493 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.58 % Allowed : 16.58 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2097 helix: 1.30 (0.28), residues: 315 sheet: -0.00 (0.23), residues: 468 loop : -1.30 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 21 HIS 0.006 0.001 HIS D 142 PHE 0.022 0.002 PHE B 263 TYR 0.026 0.001 TYR D 157 ARG 0.013 0.001 ARG F 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.95 seconds wall clock time: 59 minutes 10.83 seconds (3550.83 seconds total)