Starting phenix.real_space_refine on Mon Dec 11 05:09:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/12_2023/6mlm_9139.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/12_2023/6mlm_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_9139/12_2023/6mlm_9139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/12_2023/6mlm_9139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/12_2023/6mlm_9139.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlm_9139/12_2023/6mlm_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-1.21rc1-5172/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: 9.34, per 1000 atoms: 0.56 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: 7.08 Conformation dependent library (CDL) restraints added in 2.9 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: 2.32 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: 5.50 Time building geometry restraints manager: 7.55 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: 0.860 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: 4.720 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 47.010 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.220 ------------------------------------------------------------------------------- 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 : 2.055 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 outliers start: 6 outliers final: 1 residues processed: 509 average time/residue: 0.3683 time to fit residues: 262.0174 Evaluate side-chains 259 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1532 time to fit residues: 2.9399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7421 moved from start: 0.2870 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= 0.230 Angle : 0.708 10.987 23061 Z= 0.376 Chirality : 0.045 0.235 2517 Planarity : 0.004 0.044 3009 Dihedral : 6.223 63.665 2493 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.69 % Allowed : 8.13 % Favored : 89.18 % 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: 0.22 (0.18), residues: 2097 helix: 1.23 (0.27), residues: 327 sheet: 0.92 (0.21), residues: 546 loop : -0.50 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 21 HIS 0.006 0.001 HIS C 142 PHE 0.024 0.002 PHE C 138 TYR 0.020 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 341 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 292 time to evaluate : 2.224 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 outliers start: 49 outliers final: 22 residues processed: 316 average time/residue: 0.3141 time to fit residues: 147.6970 Evaluate side-chains 254 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 232 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2160 time to fit residues: 10.5894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 203 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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: 0.7516 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17049 Z= 0.274 Angle : 0.666 10.255 23061 Z= 0.350 Chirality : 0.043 0.193 2517 Planarity : 0.004 0.043 3009 Dihedral : 5.984 59.994 2493 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.31 % Allowed : 9.88 % Favored : 87.81 % 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: -0.06 (0.18), residues: 2097 helix: 1.20 (0.27), residues: 318 sheet: 0.83 (0.22), residues: 507 loop : -0.75 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 21 HIS 0.005 0.001 HIS C 142 PHE 0.024 0.002 PHE L 71 TYR 0.016 0.002 TYR D 157 ARG 0.007 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 286 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 261 average time/residue: 0.2794 time to fit residues: 112.3374 Evaluate side-chains 229 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.998 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1732 time to fit residues: 9.2134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** D 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17049 Z= 0.195 Angle : 0.629 9.095 23061 Z= 0.327 Chirality : 0.042 0.198 2517 Planarity : 0.004 0.046 3009 Dihedral : 5.708 48.301 2493 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.54 % Allowed : 12.14 % Favored : 86.33 % 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: -0.22 (0.18), residues: 2097 helix: 1.08 (0.28), residues: 318 sheet: 0.76 (0.22), residues: 495 loop : -0.86 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 21 HIS 0.004 0.001 HIS J 142 PHE 0.031 0.002 PHE L 71 TYR 0.017 0.001 TYR D 157 ARG 0.009 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 262 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 247 average time/residue: 0.2928 time to fit residues: 109.9229 Evaluate side-chains 226 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1701 time to fit residues: 6.2593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.0570 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- 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** D 106 HIS F 6 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 17049 Z= 0.478 Angle : 0.786 9.340 23061 Z= 0.411 Chirality : 0.046 0.262 2517 Planarity : 0.005 0.038 3009 Dihedral : 6.608 41.216 2493 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.31 % Allowed : 13.56 % Favored : 84.13 % 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: -1.09 (0.17), residues: 2097 helix: 0.49 (0.27), residues: 318 sheet: -0.04 (0.21), residues: 498 loop : -1.37 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 21 HIS 0.007 0.002 HIS H 199 PHE 0.037 0.003 PHE L 71 TYR 0.027 0.003 TYR F 33 ARG 0.017 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 269 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 2.085 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 247 average time/residue: 0.2894 time to fit residues: 108.4299 Evaluate side-chains 233 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2017 time to fit residues: 10.3742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 200 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4509 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= 0.216 Angle : 0.637 9.167 23061 Z= 0.330 Chirality : 0.043 0.159 2517 Planarity : 0.004 0.042 3009 Dihedral : 6.056 43.663 2493 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.70 % Allowed : 14.11 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.17), residues: 2097 helix: 0.80 (0.27), residues: 318 sheet: -0.01 (0.22), residues: 528 loop : -1.18 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 21 HIS 0.005 0.001 HIS C 142 PHE 0.021 0.002 PHE A 263 TYR 0.020 0.001 TYR C 157 ARG 0.009 0.000 ARG J 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 258 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 1.953 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 243 average time/residue: 0.3134 time to fit residues: 114.5694 Evaluate side-chains 216 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1731 time to fit residues: 6.7406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 0.0470 chunk 111 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7523 moved from start: 0.4597 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= 0.162 Angle : 0.599 8.917 23061 Z= 0.311 Chirality : 0.042 0.171 2517 Planarity : 0.004 0.043 3009 Dihedral : 5.608 34.873 2493 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.37 % Allowed : 14.88 % Favored : 83.75 % 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: -0.65 (0.18), residues: 2097 helix: 1.04 (0.28), residues: 318 sheet: 0.39 (0.23), residues: 462 loop : -1.16 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 21 HIS 0.004 0.001 HIS C 142 PHE 0.016 0.001 PHE A 298 TYR 0.018 0.001 TYR C 157 ARG 0.010 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 255 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 7 residues processed: 240 average time/residue: 0.3156 time to fit residues: 112.0491 Evaluate side-chains 212 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 205 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2094 time to fit residues: 5.0901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN H 312 ASN ** 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: 0.7574 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17049 Z= 0.250 Angle : 0.649 8.841 23061 Z= 0.335 Chirality : 0.044 0.471 2517 Planarity : 0.005 0.076 3009 Dihedral : 5.675 31.337 2493 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.48 % Allowed : 15.65 % 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: -0.77 (0.18), residues: 2097 helix: 0.98 (0.28), residues: 318 sheet: 0.29 (0.23), residues: 471 loop : -1.25 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 21 HIS 0.005 0.001 HIS D 142 PHE 0.022 0.002 PHE E 63 TYR 0.013 0.001 TYR I 49 ARG 0.011 0.001 ARG F 38 *********************** 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 243 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 230 average time/residue: 0.2952 time to fit residues: 102.8553 Evaluate side-chains 218 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 1.956 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1629 time to fit residues: 6.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 20.0000 chunk 191 optimal weight: 0.0000 chunk 174 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 80 optimal weight: 0.0770 chunk 145 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 122 optimal weight: 0.0970 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17049 Z= 0.162 Angle : 0.612 9.051 23061 Z= 0.317 Chirality : 0.043 0.436 2517 Planarity : 0.004 0.044 3009 Dihedral : 5.435 41.015 2493 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.27 % Allowed : 16.97 % 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: -0.53 (0.18), residues: 2097 helix: 1.16 (0.29), residues: 321 sheet: 0.50 (0.24), residues: 456 loop : -1.11 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 47 HIS 0.005 0.001 HIS C 142 PHE 0.017 0.001 PHE A 298 TYR 0.020 0.001 TYR F 32 ARG 0.014 0.000 ARG F 38 *********************** 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 235 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 231 average time/residue: 0.3048 time to fit residues: 105.8970 Evaluate side-chains 204 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1459 time to fit residues: 2.9657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN E 6 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4950 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= 0.276 Angle : 0.661 8.747 23061 Z= 0.343 Chirality : 0.044 0.465 2517 Planarity : 0.005 0.069 3009 Dihedral : 5.463 27.083 2493 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.71 % Allowed : 17.19 % Favored : 82.10 % 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: -0.81 (0.18), residues: 2097 helix: 0.96 (0.28), residues: 321 sheet: 0.07 (0.23), residues: 504 loop : -1.24 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 47 HIS 0.006 0.001 HIS D 142 PHE 0.020 0.002 PHE A 263 TYR 0.019 0.002 TYR J 94 ARG 0.013 0.001 ARG K 38 ********************** 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 221 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 208 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 210 average time/residue: 0.2904 time to fit residues: 93.7201 Evaluate side-chains 206 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2352 time to fit residues: 4.4406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.150900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125882 restraints weight = 36852.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126445 restraints weight = 25916.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127292 restraints weight = 21204.547| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17049 Z= 0.235 Angle : 0.648 9.230 23061 Z= 0.338 Chirality : 0.044 0.388 2517 Planarity : 0.004 0.064 3009 Dihedral : 5.418 26.294 2493 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.33 % Allowed : 18.07 % Favored : 81.60 % 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: 0.93 (0.28), residues: 321 sheet: 0.02 (0.23), residues: 504 loop : -1.24 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 47 HIS 0.006 0.001 HIS D 142 PHE 0.020 0.002 PHE E 63 TYR 0.018 0.002 TYR D 94 ARG 0.011 0.001 ARG C 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3382.71 seconds wall clock time: 62 minutes 46.05 seconds (3766.05 seconds total)