Starting phenix.real_space_refine on Thu Feb 15 23:25:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci1_16665/02_2024/8ci1_16665_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci1_16665/02_2024/8ci1_16665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci1_16665/02_2024/8ci1_16665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci1_16665/02_2024/8ci1_16665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci1_16665/02_2024/8ci1_16665_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ci1_16665/02_2024/8ci1_16665_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8625 2.51 5 N 2305 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13595 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "B" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "C" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "D" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "E" Number of atoms: 1736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 208, 1729 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} bond proxies already assigned to first conformer: 1775 Chain: "F" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 915 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'NCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.74, per 1000 atoms: 0.79 Number of scatterers: 13595 At special positions: 0 Unit cell: (92.88, 94.6, 117.82, 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 70 16.00 O 2595 8.00 N 2305 7.00 C 8625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 95 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 95 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 95 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 95 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 95 " - pdb=" SG CYS J 114 " 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 BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 3.7 seconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 45 sheets defined 4.8% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.197A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.577A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 173 through 175 Processing sheet with id= G, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.196A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= I, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= J, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= K, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.576A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 173 through 175 Processing sheet with id= M, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.196A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= O, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= P, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= Q, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.577A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 173 through 175 Processing sheet with id= S, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.195A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= U, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= V, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= W, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.577A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 173 through 175 Processing sheet with id= Y, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.197A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= AA, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= AB, first strand: chain 'E' and resid 76 through 79 Processing sheet with id= AC, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.576A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 173 through 175 Processing sheet with id= AE, first strand: chain 'F' and resid 3 through 7 Processing sheet with id= AF, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.241A pdb=" N THR F 121 " --> pdb=" O VAL F 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.750A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 3 through 7 Processing sheet with id= AI, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.241A pdb=" N THR G 121 " --> pdb=" O VAL G 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.750A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AL, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.242A pdb=" N THR H 121 " --> pdb=" O VAL H 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 118 through 120 removed outlier: 3.750A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 3 through 7 Processing sheet with id= AO, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.241A pdb=" N THR I 121 " --> pdb=" O VAL I 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'I' and resid 118 through 120 removed outlier: 3.750A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 3 through 7 Processing sheet with id= AR, first strand: chain 'J' and resid 11 through 13 removed outlier: 6.241A pdb=" N THR J 121 " --> pdb=" O VAL J 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'J' and resid 118 through 120 removed outlier: 3.750A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1020 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: 3.66 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4360 1.34 - 1.46: 3580 1.46 - 1.58: 5935 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 13970 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.85e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 ... (remaining 13965 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 571 107.34 - 114.00: 7581 114.00 - 120.66: 5169 120.66 - 127.32: 5474 127.32 - 133.98: 180 Bond angle restraints: 18975 Sorted by residual: angle pdb=" N VAL J 64 " pdb=" CA VAL J 64 " pdb=" C VAL J 64 " ideal model delta sigma weight residual 113.20 108.32 4.88 9.60e-01 1.09e+00 2.58e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.20 108.34 4.86 9.60e-01 1.09e+00 2.56e+01 angle pdb=" N VAL F 64 " pdb=" CA VAL F 64 " pdb=" C VAL F 64 " ideal model delta sigma weight residual 113.20 108.35 4.85 9.60e-01 1.09e+00 2.55e+01 angle pdb=" N VAL I 64 " pdb=" CA VAL I 64 " pdb=" C VAL I 64 " ideal model delta sigma weight residual 113.20 108.36 4.84 9.60e-01 1.09e+00 2.54e+01 angle pdb=" N VAL G 64 " pdb=" CA VAL G 64 " pdb=" C VAL G 64 " ideal model delta sigma weight residual 113.20 108.38 4.82 9.60e-01 1.09e+00 2.52e+01 ... (remaining 18970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 8105 14.77 - 29.53: 269 29.53 - 44.30: 86 44.30 - 59.06: 40 59.06 - 73.83: 5 Dihedral angle restraints: 8505 sinusoidal: 3685 harmonic: 4820 Sorted by residual: dihedral pdb=" N GLN J 39 " pdb=" CA GLN J 39 " pdb=" CB GLN J 39 " pdb=" CG GLN J 39 " ideal model delta sinusoidal sigma weight residual -180.00 -128.13 -51.87 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" N GLN G 39 " pdb=" CA GLN G 39 " pdb=" CB GLN G 39 " pdb=" CG GLN G 39 " ideal model delta sinusoidal sigma weight residual -180.00 -128.15 -51.85 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" N GLN F 39 " pdb=" CA GLN F 39 " pdb=" CB GLN F 39 " pdb=" CG GLN F 39 " ideal model delta sinusoidal sigma weight residual 180.00 -128.15 -51.85 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 8502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1527 0.038 - 0.075: 319 0.075 - 0.113: 161 0.113 - 0.151: 23 0.151 - 0.188: 5 Chirality restraints: 2035 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 110 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 110 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2032 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 97 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO J 98 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO J 98 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO J 98 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 97 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO H 98 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO H 98 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 98 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 97 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO I 98 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO I 98 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 98 " -0.017 5.00e-02 4.00e+02 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 261 2.68 - 3.23: 11914 3.23 - 3.79: 19392 3.79 - 4.34: 28199 4.34 - 4.90: 47325 Nonbonded interactions: 107091 Sorted by model distance: nonbonded pdb=" O TYR J 32 " pdb=" NH2 ARG J 72 " model vdw 2.122 2.520 nonbonded pdb=" O TYR F 32 " pdb=" NH2 ARG F 72 " model vdw 2.122 2.520 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 72 " model vdw 2.122 2.520 nonbonded pdb=" O TYR G 32 " pdb=" NH2 ARG G 72 " model vdw 2.122 2.520 nonbonded pdb=" O TYR I 32 " pdb=" NH2 ARG I 72 " model vdw 2.122 2.520 ... (remaining 107086 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' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 208 or resid 401 throug \ h 403)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 6.210 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.320 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 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 : 0.002 0.039 13970 Z= 0.161 Angle : 0.467 5.079 18975 Z= 0.258 Chirality : 0.041 0.188 2035 Planarity : 0.003 0.031 2430 Dihedral : 9.050 73.830 5380 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.70 % Allowed : 3.28 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.20), residues: 1645 helix: 3.04 (0.75), residues: 55 sheet: 0.74 (0.19), residues: 700 loop : -0.81 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 59 HIS 0.002 0.000 HIS A 62 PHE 0.006 0.001 PHE H 47 TYR 0.008 0.001 TYR A 117 ARG 0.001 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 321 time to evaluate : 1.735 Fit side-chains REVERT: A 46 ASN cc_start: 0.9327 (m110) cc_final: 0.8932 (m-40) REVERT: B 46 ASN cc_start: 0.9363 (m110) cc_final: 0.9077 (m-40) REVERT: D 98 ARG cc_start: 0.9121 (mtm180) cc_final: 0.8862 (mtm180) REVERT: F 13 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7901 (mm-40) REVERT: F 16 ASP cc_start: 0.8787 (m-30) cc_final: 0.8386 (m-30) REVERT: F 39 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8526 (tp-100) REVERT: F 76 LYS cc_start: 0.9391 (mptt) cc_final: 0.9191 (mtmm) REVERT: F 85 ASN cc_start: 0.9247 (t0) cc_final: 0.8673 (t0) REVERT: F 87 LYS cc_start: 0.9373 (mttt) cc_final: 0.9113 (mttm) REVERT: G 13 GLN cc_start: 0.8446 (tp-100) cc_final: 0.7847 (mm-40) REVERT: G 16 ASP cc_start: 0.8705 (m-30) cc_final: 0.8262 (m-30) REVERT: G 76 LYS cc_start: 0.9400 (mptt) cc_final: 0.9169 (mtmm) REVERT: G 85 ASN cc_start: 0.9258 (t0) cc_final: 0.8634 (t0) REVERT: G 87 LYS cc_start: 0.9366 (mttt) cc_final: 0.9111 (mttm) REVERT: H 13 GLN cc_start: 0.8439 (tp-100) cc_final: 0.7761 (mm-40) REVERT: H 16 ASP cc_start: 0.8688 (m-30) cc_final: 0.8246 (m-30) REVERT: H 39 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8649 (tp-100) REVERT: I 13 GLN cc_start: 0.8409 (tp-100) cc_final: 0.7938 (mm-40) REVERT: I 16 ASP cc_start: 0.8709 (m-30) cc_final: 0.8420 (m-30) REVERT: I 39 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8667 (tp-100) REVERT: I 76 LYS cc_start: 0.9427 (mptt) cc_final: 0.9190 (mtmm) REVERT: I 85 ASN cc_start: 0.9238 (t0) cc_final: 0.8714 (t0) REVERT: I 87 LYS cc_start: 0.9301 (mttt) cc_final: 0.9012 (mttm) REVERT: J 13 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7793 (mm-40) REVERT: J 16 ASP cc_start: 0.8795 (m-30) cc_final: 0.8383 (m-30) REVERT: J 39 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8657 (tp-100) REVERT: J 76 LYS cc_start: 0.9401 (mptt) cc_final: 0.9186 (mtmm) REVERT: J 85 ASN cc_start: 0.9271 (t0) cc_final: 0.8576 (t0) REVERT: J 87 LYS cc_start: 0.9340 (mttt) cc_final: 0.9066 (mttp) outliers start: 10 outliers final: 1 residues processed: 326 average time/residue: 1.7844 time to fit residues: 618.8598 Evaluate side-chains 265 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 52 ASN B 26 GLN B 52 ASN C 26 GLN C 52 ASN D 26 GLN D 52 ASN E 26 GLN E 52 ASN F 3 GLN F 13 GLN F 116 GLN G 13 GLN H 3 GLN H 13 GLN H 85 ASN H 116 GLN I 3 GLN I 13 GLN I 116 GLN J 3 GLN J 13 GLN J 116 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13970 Z= 0.209 Angle : 0.615 7.974 18975 Z= 0.299 Chirality : 0.047 0.353 2035 Planarity : 0.005 0.035 2430 Dihedral : 6.256 39.216 2318 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.05 % Allowed : 11.71 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.19), residues: 1645 helix: 3.12 (0.78), residues: 55 sheet: 0.65 (0.19), residues: 710 loop : -1.01 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 133 HIS 0.003 0.001 HIS A 62 PHE 0.024 0.001 PHE A 134 TYR 0.011 0.001 TYR E 117 ARG 0.007 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 275 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9400 (m110) cc_final: 0.9082 (m-40) REVERT: A 75 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9094 (mtpp) REVERT: B 46 ASN cc_start: 0.9434 (m110) cc_final: 0.9113 (m-40) REVERT: B 75 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8778 (mtpp) REVERT: F 13 GLN cc_start: 0.8365 (tp40) cc_final: 0.7832 (tp-100) REVERT: F 39 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8454 (tp-100) REVERT: F 85 ASN cc_start: 0.9288 (t0) cc_final: 0.8870 (t0) REVERT: F 87 LYS cc_start: 0.9385 (mttt) cc_final: 0.9019 (mttp) REVERT: G 13 GLN cc_start: 0.8329 (tp40) cc_final: 0.7747 (tp-100) REVERT: G 85 ASN cc_start: 0.9277 (t0) cc_final: 0.8923 (t0) REVERT: H 13 GLN cc_start: 0.8283 (tp40) cc_final: 0.7725 (tp-100) REVERT: H 39 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8545 (tp-100) REVERT: H 43 LYS cc_start: 0.8869 (mppt) cc_final: 0.8628 (mppt) REVERT: I 13 GLN cc_start: 0.8370 (tp40) cc_final: 0.7773 (tp-100) REVERT: I 39 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8507 (tp-100) REVERT: I 43 LYS cc_start: 0.8879 (mppt) cc_final: 0.8675 (mppt) REVERT: I 85 ASN cc_start: 0.9257 (t0) cc_final: 0.9053 (t0) REVERT: J 13 GLN cc_start: 0.8312 (tp40) cc_final: 0.7745 (tp-100) REVERT: J 85 ASN cc_start: 0.9293 (t0) cc_final: 0.9069 (t0) outliers start: 15 outliers final: 1 residues processed: 281 average time/residue: 1.9207 time to fit residues: 571.4885 Evaluate side-chains 265 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain F residue 109 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN E 52 ASN G 39 GLN H 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9204 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13970 Z= 0.326 Angle : 0.620 6.936 18975 Z= 0.312 Chirality : 0.049 0.363 2035 Planarity : 0.005 0.034 2430 Dihedral : 5.709 33.293 2315 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.39 % Allowed : 11.71 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.19), residues: 1645 helix: 3.53 (0.73), residues: 50 sheet: 0.61 (0.19), residues: 710 loop : -1.21 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 133 HIS 0.004 0.001 HIS D 62 PHE 0.025 0.002 PHE A 134 TYR 0.010 0.001 TYR C 92 ARG 0.007 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9411 (m110) cc_final: 0.9084 (m-40) REVERT: A 75 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9159 (mtpp) REVERT: A 98 ARG cc_start: 0.9175 (mtm180) cc_final: 0.8967 (mtm180) REVERT: B 46 ASN cc_start: 0.9442 (m110) cc_final: 0.9101 (m-40) REVERT: E 70 GLU cc_start: 0.8263 (mp0) cc_final: 0.7899 (mp0) REVERT: F 13 GLN cc_start: 0.8246 (tp40) cc_final: 0.7922 (tp-100) REVERT: F 85 ASN cc_start: 0.9337 (t0) cc_final: 0.8946 (t0) REVERT: G 13 GLN cc_start: 0.8192 (tp40) cc_final: 0.7945 (tp-100) REVERT: G 85 ASN cc_start: 0.9325 (t0) cc_final: 0.8856 (t0) REVERT: G 87 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8908 (mttp) REVERT: H 13 GLN cc_start: 0.8165 (tp40) cc_final: 0.7906 (tp-100) REVERT: H 76 LYS cc_start: 0.9334 (mtmm) cc_final: 0.8920 (mtmm) REVERT: I 13 GLN cc_start: 0.8183 (tp40) cc_final: 0.7895 (tp-100) REVERT: I 85 ASN cc_start: 0.9324 (t0) cc_final: 0.9080 (t0) REVERT: J 13 GLN cc_start: 0.8194 (tp40) cc_final: 0.7918 (tp-100) REVERT: J 76 LYS cc_start: 0.9400 (mtmm) cc_final: 0.9090 (mtmm) REVERT: J 85 ASN cc_start: 0.9357 (t0) cc_final: 0.8895 (t0) outliers start: 20 outliers final: 2 residues processed: 266 average time/residue: 2.0662 time to fit residues: 580.7746 Evaluate side-chains 258 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 254 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain G residue 87 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9171 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13970 Z= 0.185 Angle : 0.590 6.427 18975 Z= 0.294 Chirality : 0.045 0.305 2035 Planarity : 0.005 0.052 2430 Dihedral : 5.557 33.563 2315 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.39 % Allowed : 13.03 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.19), residues: 1645 helix: 3.87 (0.74), residues: 50 sheet: 0.74 (0.19), residues: 695 loop : -1.34 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 133 HIS 0.002 0.000 HIS A 62 PHE 0.026 0.001 PHE A 134 TYR 0.009 0.001 TYR E 117 ARG 0.011 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9406 (m110) cc_final: 0.9065 (m-40) REVERT: A 75 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9106 (mtpp) REVERT: B 46 ASN cc_start: 0.9435 (m110) cc_final: 0.9114 (m-40) REVERT: C 98 ARG cc_start: 0.9147 (mtm180) cc_final: 0.8945 (mtm180) REVERT: E 70 GLU cc_start: 0.8290 (mp0) cc_final: 0.7867 (mp0) REVERT: E 75 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9125 (mtpp) REVERT: F 13 GLN cc_start: 0.8140 (tp40) cc_final: 0.7876 (tp-100) REVERT: F 85 ASN cc_start: 0.9345 (t0) cc_final: 0.8945 (t0) REVERT: G 85 ASN cc_start: 0.9329 (t0) cc_final: 0.8832 (t0) REVERT: G 87 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8863 (mttp) REVERT: H 13 GLN cc_start: 0.8089 (tp40) cc_final: 0.7876 (tp-100) REVERT: H 76 LYS cc_start: 0.9352 (mtmm) cc_final: 0.8825 (mtmm) REVERT: H 85 ASN cc_start: 0.9268 (t0) cc_final: 0.8773 (t0) REVERT: I 13 GLN cc_start: 0.8112 (tp40) cc_final: 0.7874 (tp-100) REVERT: I 85 ASN cc_start: 0.9301 (t0) cc_final: 0.9049 (t0) REVERT: J 13 GLN cc_start: 0.8104 (tp40) cc_final: 0.7864 (tp-100) REVERT: J 76 LYS cc_start: 0.9382 (mtmm) cc_final: 0.9050 (mtmm) REVERT: J 85 ASN cc_start: 0.9348 (t0) cc_final: 0.8887 (t0) outliers start: 20 outliers final: 4 residues processed: 273 average time/residue: 1.8329 time to fit residues: 531.0316 Evaluate side-chains 260 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 253 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain H residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13970 Z= 0.199 Angle : 0.572 7.368 18975 Z= 0.284 Chirality : 0.045 0.351 2035 Planarity : 0.005 0.043 2430 Dihedral : 5.386 31.926 2315 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.91 % Allowed : 13.73 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.19), residues: 1645 helix: 3.77 (0.73), residues: 50 sheet: 0.83 (0.19), residues: 695 loop : -1.38 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 133 HIS 0.002 0.000 HIS A 62 PHE 0.027 0.001 PHE A 134 TYR 0.010 0.001 TYR I 94 ARG 0.009 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 260 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9403 (m110) cc_final: 0.9059 (m-40) REVERT: A 70 GLU cc_start: 0.8620 (mp0) cc_final: 0.8415 (mp0) REVERT: A 75 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9120 (mtpp) REVERT: A 98 ARG cc_start: 0.9080 (mtm180) cc_final: 0.8873 (mtm180) REVERT: B 46 ASN cc_start: 0.9430 (m110) cc_final: 0.9104 (m-40) REVERT: E 70 GLU cc_start: 0.8324 (mp0) cc_final: 0.8105 (mp0) REVERT: F 13 GLN cc_start: 0.8144 (tp40) cc_final: 0.7849 (tp-100) REVERT: F 73 ASP cc_start: 0.8475 (t70) cc_final: 0.8170 (t0) REVERT: F 85 ASN cc_start: 0.9354 (t0) cc_final: 0.8935 (t0) REVERT: G 73 ASP cc_start: 0.8504 (t70) cc_final: 0.7579 (t0) REVERT: G 85 ASN cc_start: 0.9348 (t0) cc_final: 0.8940 (t0) REVERT: H 13 GLN cc_start: 0.8042 (tp40) cc_final: 0.7831 (tp-100) REVERT: H 85 ASN cc_start: 0.9261 (t0) cc_final: 0.8767 (t0) REVERT: I 13 GLN cc_start: 0.8148 (tp40) cc_final: 0.7921 (tp-100) REVERT: I 76 LYS cc_start: 0.9296 (mtmm) cc_final: 0.8887 (mtmm) REVERT: I 85 ASN cc_start: 0.9308 (t0) cc_final: 0.9042 (t0) REVERT: J 13 GLN cc_start: 0.8127 (tp40) cc_final: 0.7879 (tp-100) REVERT: J 76 LYS cc_start: 0.9386 (mtmm) cc_final: 0.8972 (mtmm) REVERT: J 85 ASN cc_start: 0.9346 (t0) cc_final: 0.8895 (t0) outliers start: 13 outliers final: 6 residues processed: 266 average time/residue: 1.9041 time to fit residues: 537.0940 Evaluate side-chains 262 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 255 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9171 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13970 Z= 0.201 Angle : 0.589 6.764 18975 Z= 0.294 Chirality : 0.044 0.321 2035 Planarity : 0.005 0.042 2430 Dihedral : 5.326 31.221 2315 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.25 % Allowed : 15.12 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.19), residues: 1645 helix: 3.80 (0.73), residues: 50 sheet: 0.71 (0.19), residues: 720 loop : -1.33 (0.17), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 133 HIS 0.002 0.000 HIS A 62 PHE 0.027 0.001 PHE A 134 TYR 0.008 0.001 TYR I 94 ARG 0.009 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9397 (m110) cc_final: 0.9048 (m-40) REVERT: A 75 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9106 (mtpp) REVERT: B 46 ASN cc_start: 0.9421 (m110) cc_final: 0.9093 (m-40) REVERT: E 70 GLU cc_start: 0.8337 (mp0) cc_final: 0.8090 (mp0) REVERT: F 13 GLN cc_start: 0.8144 (tp40) cc_final: 0.7842 (tp-100) REVERT: F 73 ASP cc_start: 0.8490 (t70) cc_final: 0.8188 (t0) REVERT: F 85 ASN cc_start: 0.9361 (t0) cc_final: 0.8934 (t0) REVERT: G 76 LYS cc_start: 0.9381 (mtmm) cc_final: 0.8939 (mtmm) REVERT: G 85 ASN cc_start: 0.9349 (t0) cc_final: 0.9094 (t0) REVERT: H 13 GLN cc_start: 0.8029 (tp40) cc_final: 0.7824 (tp-100) REVERT: H 85 ASN cc_start: 0.9278 (t0) cc_final: 0.8791 (t0) REVERT: I 13 GLN cc_start: 0.8133 (tp40) cc_final: 0.7926 (tp-100) REVERT: I 76 LYS cc_start: 0.9311 (mtmm) cc_final: 0.8859 (mtmm) REVERT: I 85 ASN cc_start: 0.9313 (t0) cc_final: 0.9038 (t0) REVERT: J 13 GLN cc_start: 0.8117 (tp40) cc_final: 0.7881 (tp-100) REVERT: J 43 LYS cc_start: 0.8984 (mppt) cc_final: 0.8769 (mppt) REVERT: J 76 LYS cc_start: 0.9385 (mtmm) cc_final: 0.8953 (mtmm) REVERT: J 85 ASN cc_start: 0.9340 (t0) cc_final: 0.8902 (t0) outliers start: 18 outliers final: 8 residues processed: 268 average time/residue: 1.9206 time to fit residues: 545.6393 Evaluate side-chains 262 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN G 116 GLN H 3 GLN J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13970 Z= 0.163 Angle : 0.561 7.486 18975 Z= 0.279 Chirality : 0.044 0.301 2035 Planarity : 0.005 0.048 2430 Dihedral : 5.176 30.369 2315 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.05 % Allowed : 15.47 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.19), residues: 1645 helix: 3.01 (0.76), residues: 55 sheet: 0.77 (0.19), residues: 720 loop : -1.40 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 133 HIS 0.001 0.000 HIS D 62 PHE 0.028 0.001 PHE D 134 TYR 0.008 0.001 TYR E 117 ARG 0.011 0.001 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 256 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9392 (m110) cc_final: 0.9046 (m-40) REVERT: A 75 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9103 (mtpp) REVERT: B 46 ASN cc_start: 0.9405 (m110) cc_final: 0.9076 (m-40) REVERT: E 70 GLU cc_start: 0.8341 (mp0) cc_final: 0.8079 (mp0) REVERT: F 13 GLN cc_start: 0.8139 (tp40) cc_final: 0.7853 (tp-100) REVERT: F 73 ASP cc_start: 0.8499 (t70) cc_final: 0.8196 (t0) REVERT: F 85 ASN cc_start: 0.9361 (t0) cc_final: 0.8939 (t0) REVERT: G 76 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9032 (mtmm) REVERT: G 85 ASN cc_start: 0.9338 (t0) cc_final: 0.9094 (t0) REVERT: H 13 GLN cc_start: 0.8020 (tp40) cc_final: 0.7820 (tp-100) REVERT: H 39 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8409 (tp-100) REVERT: H 43 LYS cc_start: 0.8834 (mppt) cc_final: 0.8563 (mppt) REVERT: H 85 ASN cc_start: 0.9284 (t0) cc_final: 0.8798 (t0) REVERT: I 13 GLN cc_start: 0.8135 (tp40) cc_final: 0.7928 (tp-100) REVERT: I 76 LYS cc_start: 0.9309 (mtmm) cc_final: 0.8930 (mtmm) REVERT: I 85 ASN cc_start: 0.9305 (t0) cc_final: 0.9018 (t0) REVERT: J 13 GLN cc_start: 0.8103 (tp40) cc_final: 0.7869 (tp-100) REVERT: J 76 LYS cc_start: 0.9390 (mtmm) cc_final: 0.8946 (mtmm) REVERT: J 85 ASN cc_start: 0.9335 (t0) cc_final: 0.8904 (t0) outliers start: 15 outliers final: 9 residues processed: 266 average time/residue: 1.9200 time to fit residues: 540.9332 Evaluate side-chains 263 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 253 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 8.9990 chunk 61 optimal weight: 0.0170 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN F 3 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9195 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13970 Z= 0.267 Angle : 0.620 7.871 18975 Z= 0.311 Chirality : 0.045 0.300 2035 Planarity : 0.005 0.051 2430 Dihedral : 5.300 28.211 2315 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.05 % Allowed : 15.82 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.19), residues: 1645 helix: 3.68 (0.72), residues: 50 sheet: 0.72 (0.19), residues: 720 loop : -1.30 (0.17), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 133 HIS 0.003 0.001 HIS A 62 PHE 0.029 0.001 PHE B 134 TYR 0.007 0.001 TYR C 92 ARG 0.012 0.001 ARG J 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9397 (m110) cc_final: 0.9039 (m-40) REVERT: A 75 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9128 (mtpp) REVERT: B 46 ASN cc_start: 0.9429 (m110) cc_final: 0.9088 (m-40) REVERT: E 70 GLU cc_start: 0.8403 (mp0) cc_final: 0.8108 (mp0) REVERT: F 13 GLN cc_start: 0.8205 (tp40) cc_final: 0.7901 (tp-100) REVERT: F 73 ASP cc_start: 0.8562 (t70) cc_final: 0.8196 (t0) REVERT: F 85 ASN cc_start: 0.9380 (t0) cc_final: 0.8892 (t0) REVERT: G 76 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9037 (mtmm) REVERT: H 13 GLN cc_start: 0.8032 (tp40) cc_final: 0.7806 (tp-100) REVERT: H 76 LYS cc_start: 0.9260 (mtmm) cc_final: 0.9034 (mtmm) REVERT: H 85 ASN cc_start: 0.9306 (t0) cc_final: 0.8804 (t0) REVERT: I 13 GLN cc_start: 0.8184 (tp40) cc_final: 0.7972 (tp-100) REVERT: I 76 LYS cc_start: 0.9304 (mtmm) cc_final: 0.8799 (mtmm) REVERT: I 85 ASN cc_start: 0.9343 (t0) cc_final: 0.9059 (t0) REVERT: J 13 GLN cc_start: 0.8147 (tp40) cc_final: 0.7926 (tp-100) REVERT: J 43 LYS cc_start: 0.9062 (mppt) cc_final: 0.8843 (mppt) REVERT: J 76 LYS cc_start: 0.9396 (mtmm) cc_final: 0.8940 (mtmm) REVERT: J 85 ASN cc_start: 0.9331 (t0) cc_final: 0.8897 (t0) outliers start: 15 outliers final: 8 residues processed: 261 average time/residue: 1.8641 time to fit residues: 515.7478 Evaluate side-chains 259 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 250 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 112 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN G 13 GLN H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13970 Z= 0.200 Angle : 0.583 8.614 18975 Z= 0.291 Chirality : 0.044 0.287 2035 Planarity : 0.005 0.053 2430 Dihedral : 5.244 28.798 2315 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.05 % Allowed : 15.54 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.19), residues: 1645 helix: 3.79 (0.72), residues: 50 sheet: 0.74 (0.19), residues: 720 loop : -1.30 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 133 HIS 0.002 0.000 HIS A 62 PHE 0.030 0.001 PHE A 134 TYR 0.007 0.001 TYR E 117 ARG 0.013 0.001 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9392 (m110) cc_final: 0.9043 (m-40) REVERT: A 75 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9106 (mtpp) REVERT: B 46 ASN cc_start: 0.9411 (m110) cc_final: 0.9054 (m-40) REVERT: E 70 GLU cc_start: 0.8396 (mp0) cc_final: 0.8089 (mp0) REVERT: F 13 GLN cc_start: 0.8169 (tp40) cc_final: 0.7883 (tp-100) REVERT: F 73 ASP cc_start: 0.8585 (t70) cc_final: 0.8220 (t0) REVERT: F 85 ASN cc_start: 0.9337 (t0) cc_final: 0.8831 (t0) REVERT: G 76 LYS cc_start: 0.9419 (mtmm) cc_final: 0.9077 (mtmm) REVERT: H 13 GLN cc_start: 0.8023 (tp40) cc_final: 0.7807 (tp-100) REVERT: H 76 LYS cc_start: 0.9294 (mtmm) cc_final: 0.9071 (mtmm) REVERT: H 85 ASN cc_start: 0.9307 (t0) cc_final: 0.8804 (t0) REVERT: I 13 GLN cc_start: 0.8200 (tp40) cc_final: 0.7989 (tp-100) REVERT: I 76 LYS cc_start: 0.9308 (mtmm) cc_final: 0.8916 (mtmm) REVERT: I 85 ASN cc_start: 0.9331 (t0) cc_final: 0.9043 (t0) REVERT: J 13 GLN cc_start: 0.8145 (tp40) cc_final: 0.7923 (tp-100) REVERT: J 43 LYS cc_start: 0.9067 (mppt) cc_final: 0.8855 (mppt) REVERT: J 76 LYS cc_start: 0.9389 (mtmm) cc_final: 0.8932 (mtmm) REVERT: J 85 ASN cc_start: 0.9319 (t0) cc_final: 0.8900 (t0) outliers start: 15 outliers final: 9 residues processed: 263 average time/residue: 1.9293 time to fit residues: 537.3632 Evaluate side-chains 261 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9196 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13970 Z= 0.267 Angle : 0.624 8.082 18975 Z= 0.313 Chirality : 0.045 0.294 2035 Planarity : 0.005 0.059 2430 Dihedral : 5.306 27.684 2315 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.77 % Allowed : 16.38 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.19), residues: 1645 helix: 3.63 (0.71), residues: 50 sheet: 0.69 (0.19), residues: 720 loop : -1.29 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 133 HIS 0.003 0.001 HIS A 62 PHE 0.030 0.001 PHE E 134 TYR 0.010 0.001 TYR D 128 ARG 0.013 0.001 ARG I 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 252 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.9402 (m110) cc_final: 0.9045 (m-40) REVERT: A 75 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9128 (mtpp) REVERT: B 46 ASN cc_start: 0.9430 (m110) cc_final: 0.9074 (m-40) REVERT: C 70 GLU cc_start: 0.8373 (mp0) cc_final: 0.8103 (mp0) REVERT: E 70 GLU cc_start: 0.8437 (mp0) cc_final: 0.8123 (mp0) REVERT: F 13 GLN cc_start: 0.8200 (tp40) cc_final: 0.7899 (tp-100) REVERT: F 73 ASP cc_start: 0.8625 (t70) cc_final: 0.8262 (t0) REVERT: F 85 ASN cc_start: 0.9355 (t0) cc_final: 0.8848 (t0) REVERT: G 76 LYS cc_start: 0.9425 (mtmm) cc_final: 0.9084 (mtmm) REVERT: H 13 GLN cc_start: 0.8042 (tp40) cc_final: 0.7817 (tp-100) REVERT: H 76 LYS cc_start: 0.9285 (mtmm) cc_final: 0.9051 (mtmm) REVERT: H 85 ASN cc_start: 0.9317 (t0) cc_final: 0.8811 (t0) REVERT: I 13 GLN cc_start: 0.8216 (tp40) cc_final: 0.8002 (tp-100) REVERT: I 76 LYS cc_start: 0.9309 (mtmm) cc_final: 0.8799 (mtmm) REVERT: I 85 ASN cc_start: 0.9341 (t0) cc_final: 0.9039 (t0) REVERT: J 13 GLN cc_start: 0.8165 (tp40) cc_final: 0.7943 (tp-100) REVERT: J 43 LYS cc_start: 0.9103 (mppt) cc_final: 0.8865 (mppt) REVERT: J 76 LYS cc_start: 0.9392 (mtmm) cc_final: 0.8933 (mtmm) REVERT: J 85 ASN cc_start: 0.9315 (t0) cc_final: 0.8887 (t0) outliers start: 11 outliers final: 10 residues processed: 260 average time/residue: 1.9898 time to fit residues: 548.0814 Evaluate side-chains 263 residues out of total 1425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 252 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain F residue 95 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 95 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN H 3 GLN H 82 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.041863 restraints weight = 83388.423| |-----------------------------------------------------------------------------| r_work (start): 0.2362 rms_B_bonded: 4.87 r_work: 0.2184 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2190 r_free = 0.2190 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2190 r_free = 0.2190 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13970 Z= 0.333 Angle : 0.632 7.843 18975 Z= 0.316 Chirality : 0.047 0.299 2035 Planarity : 0.005 0.061 2430 Dihedral : 5.507 27.783 2315 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.77 % Allowed : 15.96 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.19), residues: 1645 helix: 3.38 (0.70), residues: 50 sheet: 0.64 (0.19), residues: 720 loop : -1.32 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 133 HIS 0.004 0.001 HIS A 62 PHE 0.028 0.001 PHE A 134 TYR 0.008 0.001 TYR C 92 ARG 0.013 0.001 ARG I 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7631.28 seconds wall clock time: 134 minutes 51.54 seconds (8091.54 seconds total)