Starting phenix.real_space_refine on Tue Aug 6 14:33:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/08_2024/6mlm_9139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/08_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_9139/08_2024/6mlm_9139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/08_2024/6mlm_9139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/08_2024/6mlm_9139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/08_2024/6mlm_9139.cif" } 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-5409/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: 9.05, per 1000 atoms: 0.54 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: 6.04 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: 2.88 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: 5.63 Time building geometry restraints manager: 6.66 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 3.040 nonbonded pdb=" OH TYR F 99 " pdb=" OD1 ASN G 34 " model vdw 2.372 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.320 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.800 ------------------------------------------------------------------------------- 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 : 1.860 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: 0.3673 time to fit residues: 264.5211 Evaluate side-chains 261 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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: 3.9990 chunk 156 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN I 90 GLN B 327 GLN B 338 ASN D 42 GLN D 106 HIS F 3 GLN G 90 GLN H 179 GLN H 312 ASN L 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17049 Z= 0.245 Angle : 0.726 11.169 23061 Z= 0.384 Chirality : 0.046 0.280 2517 Planarity : 0.005 0.045 3009 Dihedral : 6.364 65.621 2495 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.64 % Allowed : 7.36 % Favored : 90.01 % 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: 0.16 (0.18), residues: 2097 helix: 1.19 (0.27), residues: 333 sheet: 0.64 (0.21), residues: 576 loop : -0.45 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 14 HIS 0.006 0.001 HIS C 142 PHE 0.027 0.002 PHE D 138 TYR 0.021 0.002 TYR D 119 ARG 0.008 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 360 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 312 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.6529 (p) cc_final: 0.5770 (p) REVERT: C 149 MET cc_start: 0.4324 (tpt) cc_final: 0.3352 (ptt) REVERT: B 69 THR cc_start: 0.6689 (p) cc_final: 0.5621 (p) REVERT: D 22 TYR cc_start: 0.7702 (m-80) cc_final: 0.7320 (m-80) REVERT: D 61 GLN cc_start: 0.5784 (OUTLIER) cc_final: 0.5540 (mm110) REVERT: D 149 MET cc_start: 0.4352 (tpt) cc_final: 0.3563 (ptt) REVERT: H 69 THR cc_start: 0.6655 (p) cc_final: 0.5695 (p) REVERT: J 21 TRP cc_start: 0.5415 (m-10) cc_final: 0.5178 (m-10) REVERT: J 149 MET cc_start: 0.4738 (tpt) cc_final: 0.3952 (ptt) outliers start: 48 outliers final: 20 residues processed: 335 average time/residue: 0.2890 time to fit residues: 143.5636 Evaluate side-chains 251 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain E residue 70 THR 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 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 J residue 67 ASP Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 79 TYR Chi-restraints excluded: chain K residue 100 ASP 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: 6.9990 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN H 327 GLN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17049 Z= 0.465 Angle : 0.809 10.884 23061 Z= 0.430 Chirality : 0.047 0.240 2517 Planarity : 0.006 0.054 3009 Dihedral : 6.574 59.533 2493 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.23 % Allowed : 9.56 % Favored : 86.22 % 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: -0.75 (0.17), residues: 2097 helix: 0.80 (0.27), residues: 318 sheet: -0.04 (0.20), residues: 537 loop : -1.07 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 21 HIS 0.008 0.002 HIS H 199 PHE 0.032 0.003 PHE D 138 TYR 0.023 0.003 TYR I 49 ARG 0.022 0.001 ARG J 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 318 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 241 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 GLU cc_start: 0.2516 (mt-10) cc_final: 0.2157 (mt-10) REVERT: C 22 TYR cc_start: 0.7850 (m-80) cc_final: 0.7381 (m-80) REVERT: C 103 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8611 (mp0) REVERT: C 149 MET cc_start: 0.4454 (tpt) cc_final: 0.3648 (ppp) REVERT: D 22 TYR cc_start: 0.7384 (m-80) cc_final: 0.7043 (m-80) REVERT: D 149 MET cc_start: 0.4313 (tpt) cc_final: 0.3785 (ppp) REVERT: F 23 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8775 (mtpp) REVERT: H 263 PHE cc_start: 0.7905 (m-10) cc_final: 0.7702 (m-80) REVERT: J 21 TRP cc_start: 0.5167 (m-10) cc_final: 0.4710 (m-10) REVERT: K 46 GLU cc_start: 0.7864 (pt0) cc_final: 0.7644 (pt0) REVERT: L 70 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5268 (pp20) outliers start: 77 outliers final: 45 residues processed: 285 average time/residue: 0.2522 time to fit residues: 111.7489 Evaluate side-chains 261 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 251 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 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 70 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 37 GLU 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 258 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 67 ASP 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 G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 327 GLN 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 100 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 70 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 6 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4016 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= 0.217 Angle : 0.649 10.168 23061 Z= 0.338 Chirality : 0.043 0.185 2517 Planarity : 0.004 0.039 3009 Dihedral : 5.964 53.122 2493 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.13 % Allowed : 12.58 % Favored : 84.29 % 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: -0.66 (0.17), residues: 2097 helix: 0.87 (0.27), residues: 321 sheet: 0.20 (0.21), residues: 507 loop : -1.08 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 21 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE J 138 TYR 0.016 0.001 TYR D 157 ARG 0.007 0.000 ARG K 38 *********************** 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 : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 MET cc_start: 0.4545 (tpt) cc_final: 0.4309 (tpt) REVERT: D 149 MET cc_start: 0.4285 (tpt) cc_final: 0.3488 (ptt) REVERT: G 105 GLU cc_start: 0.7125 (mp0) cc_final: 0.6293 (mp0) REVERT: J 149 MET cc_start: 0.3808 (tpt) cc_final: 0.3038 (tpt) REVERT: K 48 MET cc_start: 0.7498 (mtm) cc_final: 0.7127 (mtp) REVERT: L 70 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5254 (pp20) outliers start: 57 outliers final: 36 residues processed: 257 average time/residue: 0.2676 time to fit residues: 105.8639 Evaluate side-chains 244 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 207 time to evaluate : 1.923 ------------------------------------------------------------------------------- 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 C residue 55 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 88 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 101 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU 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 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain D residue 67 ASP 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 G residue 11 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain H residue 41 LYS 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 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 100 ASP Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 70 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 102 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17049 Z= 0.303 Angle : 0.667 8.853 23061 Z= 0.350 Chirality : 0.043 0.194 2517 Planarity : 0.005 0.040 3009 Dihedral : 5.872 37.245 2493 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.29 % Allowed : 13.62 % Favored : 83.09 % 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: -0.87 (0.17), residues: 2097 helix: 0.73 (0.27), residues: 318 sheet: -0.01 (0.21), residues: 498 loop : -1.18 (0.17), residues: 1281 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 0.016 0.002 PHE H 263 TYR 0.017 0.002 TYR D 22 ARG 0.009 0.001 ARG E 38 *********************** 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 284 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 1.997 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: B 130 ARG cc_start: 0.6850 (ttp-110) cc_final: 0.6645 (ttm110) REVERT: D 103 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8459 (mp0) REVERT: D 120 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7879 (pp20) REVERT: G 100 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6843 (pt0) REVERT: G 105 GLU cc_start: 0.7311 (mp0) cc_final: 0.6864 (mp0) REVERT: L 70 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5342 (pp20) outliers start: 60 outliers final: 41 residues processed: 254 average time/residue: 0.2740 time to fit residues: 107.7354 Evaluate side-chains 243 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 67 ASP Chi-restraints excluded: chain C residue 88 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 I residue 4 MET Chi-restraints excluded: chain I residue 21 ILE 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 291 SER Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL 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 G residue 21 ILE Chi-restraints excluded: chain G residue 37 GLU 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 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 L residue 4 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 70 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17049 Z= 0.238 Angle : 0.628 8.986 23061 Z= 0.329 Chirality : 0.043 0.182 2517 Planarity : 0.004 0.045 3009 Dihedral : 5.639 31.242 2493 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.35 % Allowed : 13.89 % Favored : 82.76 % 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: -0.86 (0.17), residues: 2097 helix: 0.88 (0.27), residues: 318 sheet: 0.07 (0.22), residues: 474 loop : -1.24 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 21 HIS 0.005 0.001 HIS C 142 PHE 0.018 0.002 PHE H 263 TYR 0.016 0.001 TYR D 157 ARG 0.011 0.000 ARG C 54 *********************** 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 278 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 217 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.6873 (ttp-110) cc_final: 0.6640 (ttm110) REVERT: C 88 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: B 130 ARG cc_start: 0.6847 (ttp-110) cc_final: 0.6628 (ttm110) REVERT: D 120 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7864 (pp20) REVERT: G 70 GLU cc_start: 0.6121 (tm-30) cc_final: 0.5916 (tm-30) REVERT: G 100 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6828 (pt0) REVERT: H 217 LEU cc_start: 0.8551 (tt) cc_final: 0.8322 (tp) REVERT: J 149 MET cc_start: 0.3931 (tpt) cc_final: 0.3201 (tpt) REVERT: K 48 MET cc_start: 0.7410 (mtm) cc_final: 0.7044 (mtp) REVERT: L 70 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5645 (pp20) outliers start: 61 outliers final: 46 residues processed: 249 average time/residue: 0.2701 time to fit residues: 102.7995 Evaluate side-chains 250 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 201 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 263 PHE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain C residue 67 ASP 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 70 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 4 MET 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 291 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 67 ASP 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 100 ASP 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 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 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 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 L residue 4 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 70 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1496 > 50: distance: 30 - 239: 36.984 distance: 33 - 236: 29.342 distance: 78 - 192: 31.545 distance: 81 - 189: 26.142 distance: 102 - 231: 35.002 distance: 105 - 228: 28.319 distance: 152 - 185: 34.692 distance: 155 - 182: 32.076 distance: 173 - 182: 34.958 distance: 182 - 183: 44.495 distance: 183 - 184: 44.326 distance: 183 - 186: 26.954 distance: 184 - 185: 65.739 distance: 184 - 189: 41.006 distance: 186 - 187: 48.397 distance: 186 - 188: 38.046 distance: 189 - 190: 49.668 distance: 190 - 191: 15.761 distance: 190 - 193: 42.757 distance: 191 - 192: 28.315 distance: 191 - 200: 38.580 distance: 193 - 194: 27.040 distance: 194 - 195: 35.113 distance: 194 - 196: 48.218 distance: 195 - 197: 44.506 distance: 196 - 198: 42.585 distance: 197 - 199: 9.024 distance: 198 - 199: 12.629 distance: 200 - 201: 38.522 distance: 201 - 202: 14.511 distance: 201 - 204: 20.168 distance: 202 - 203: 21.913 distance: 202 - 208: 22.038 distance: 204 - 205: 6.608 distance: 205 - 206: 19.538 distance: 205 - 207: 12.599 distance: 208 - 209: 47.279 distance: 209 - 210: 44.642 distance: 210 - 211: 35.401 distance: 210 - 212: 45.788 distance: 212 - 213: 40.845 distance: 213 - 214: 33.748 distance: 213 - 216: 59.322 distance: 214 - 215: 25.196 distance: 214 - 217: 20.186 distance: 217 - 218: 33.813 distance: 218 - 219: 31.162 distance: 218 - 221: 51.819 distance: 219 - 220: 29.746 distance: 219 - 228: 29.286 distance: 221 - 222: 27.871 distance: 222 - 223: 17.361 distance: 222 - 224: 13.333 distance: 223 - 225: 32.454 distance: 224 - 226: 37.631 distance: 225 - 227: 27.479 distance: 226 - 227: 29.085 distance: 228 - 229: 49.888 distance: 229 - 230: 38.739 distance: 229 - 232: 61.987 distance: 230 - 231: 57.123 distance: 230 - 236: 8.402 distance: 232 - 233: 33.980 distance: 232 - 234: 49.914 distance: 233 - 235: 43.905 distance: 236 - 237: 50.882 distance: 237 - 238: 42.594 distance: 237 - 240: 49.033 distance: 238 - 239: 68.237 distance: 238 - 241: 40.299 distance: 241 - 242: 41.019 distance: 241 - 247: 69.808 distance: 242 - 243: 57.524 distance: 242 - 245: 57.158 distance: 243 - 244: 43.449 distance: 243 - 248: 43.667 distance: 245 - 246: 42.751 distance: 246 - 247: 41.290 distance: 248 - 249: 24.449 distance: 249 - 250: 41.945 distance: 249 - 252: 28.400 distance: 250 - 251: 39.693 distance: 250 - 256: 19.222 distance: 252 - 253: 25.407 distance: 253 - 254: 32.900 distance: 253 - 255: 16.960