Starting phenix.real_space_refine on Sat Jul 27 08:35:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to5_41435/07_2024/8to5_41435_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to5_41435/07_2024/8to5_41435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to5_41435/07_2024/8to5_41435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to5_41435/07_2024/8to5_41435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to5_41435/07_2024/8to5_41435_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to5_41435/07_2024/8to5_41435_trim.cif" } resolution = 1.87 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= -0.002 sd= 0.116 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: 5 Type Number sf(0) Gaussians S 67 5.16 5 C 11403 2.51 5 N 3151 2.21 5 O 5478 1.98 5 H 17088 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M GLU 7": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 131": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "Q GLU 7": "OE1" <-> "OE2" Residue "Q GLU 109": "OE1" <-> "OE2" Residue "Q ASP 116": "OD1" <-> "OD2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "R ASP 144": "OD1" <-> "OD2" Residue "S GLU 117": "OE1" <-> "OE2" Residue "T GLU 115": "OE1" <-> "OE2" Residue "T GLU 136": "OE1" <-> "OE2" Residue "U GLU 109": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 136": "OE1" <-> "OE2" Residue "V ASP 144": "OD1" <-> "OD2" Residue "V ASP 152": "OD1" <-> "OD2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X ASP 140": "OD1" <-> "OD2" Residue "b ASP 112": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 37187 Number of models: 1 Model: "" Number of chains: 40 Chain: "M" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "N" Number of atoms: 2546 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2534 Chain: "O" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "P" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "R" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "T" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 2455 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Conformer: "B" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} bond proxies already assigned to first conformer: 2456 Chain: "V" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "X" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 3433 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Conformer: "B" Number of residues, atoms: 216, 3433 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} bond proxies already assigned to first conformer: 3454 Chain: "c" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1134 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain breaks: 1 Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "N" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 168 Classifications: {'water': 168} Link IDs: {None: 167} Chain: "O" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 134 Classifications: {'water': 134} Link IDs: {None: 133} Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "Q" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "R" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 152 Classifications: {'water': 152} Link IDs: {None: 151} Chain: "S" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "T" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 164 Classifications: {'water': 164} Link IDs: {None: 163} Chain: "U" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "V" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "W" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "X" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "b" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "c" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Time building chain proxies: 22.85, per 1000 atoms: 0.61 Number of scatterers: 37187 At special positions: 0 Unit cell: (123.59, 122.863, 84.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 O 5478 8.00 N 3151 7.00 C 11403 6.00 H 17088 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.38 Conformation dependent library (CDL) restraints added in 4.3 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 1 sheets defined 82.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'M' and resid 3 through 15 Processing helix chain 'M' and resid 20 through 47 removed outlier: 4.558A pdb=" N ASN M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 64 through 68 Processing helix chain 'M' and resid 77 through 102 Processing helix chain 'M' and resid 104 through 111 Processing helix chain 'M' and resid 114 through 122 Processing helix chain 'M' and resid 125 through 140 removed outlier: 3.978A pdb=" N TYR M 129 " --> pdb=" O SER M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 161 Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.796A pdb=" N VAL N 8 " --> pdb=" O VAL N 4 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG N 15 " --> pdb=" O GLN N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 33 through 47 Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 75 through 100 Processing helix chain 'N' and resid 102 through 109 Processing helix chain 'N' and resid 112 through 121 Processing helix chain 'N' and resid 123 through 144 Processing helix chain 'N' and resid 153 through 172 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 20 through 47 removed outlier: 4.503A pdb=" N ASN O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 64 through 69 removed outlier: 3.516A pdb=" N GLN O 68 " --> pdb=" O PRO O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 102 Processing helix chain 'O' and resid 104 through 111 Processing helix chain 'O' and resid 114 through 122 Processing helix chain 'O' and resid 125 through 140 removed outlier: 3.963A pdb=" N TYR O 129 " --> pdb=" O SER O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 Processing helix chain 'P' and resid 3 through 16 removed outlier: 4.049A pdb=" N VAL P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG P 15 " --> pdb=" O GLN P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 33 Processing helix chain 'P' and resid 33 through 47 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 64 through 67 Processing helix chain 'P' and resid 75 through 100 Processing helix chain 'P' and resid 102 through 109 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'P' and resid 123 through 144 Processing helix chain 'P' and resid 153 through 172 Processing helix chain 'Q' and resid 3 through 15 Processing helix chain 'Q' and resid 20 through 47 removed outlier: 4.542A pdb=" N ASN Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 64 through 69 Processing helix chain 'Q' and resid 77 through 102 Processing helix chain 'Q' and resid 104 through 111 Processing helix chain 'Q' and resid 114 through 123 Processing helix chain 'Q' and resid 125 through 140 removed outlier: 4.002A pdb=" N TYR Q 129 " --> pdb=" O SER Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 162 Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.910A pdb=" N VAL R 8 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 33 Processing helix chain 'R' and resid 33 through 47 Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 64 through 67 Processing helix chain 'R' and resid 75 through 100 Processing helix chain 'R' and resid 102 through 109 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 153 through 172 Processing helix chain 'S' and resid 3 through 15 Processing helix chain 'S' and resid 20 through 47 removed outlier: 4.528A pdb=" N ASN S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA S 36 " --> pdb=" O ARG S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 64 through 68 Processing helix chain 'S' and resid 77 through 102 Processing helix chain 'S' and resid 104 through 111 Processing helix chain 'S' and resid 114 through 122 Processing helix chain 'S' and resid 125 through 140 removed outlier: 4.011A pdb=" N TYR S 129 " --> pdb=" O SER S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 162 Processing helix chain 'T' and resid 3 through 16 removed outlier: 3.829A pdb=" N VAL T 8 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 33 Processing helix chain 'T' and resid 33 through 47 Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 64 through 67 Processing helix chain 'T' and resid 75 through 100 Processing helix chain 'T' and resid 102 through 109 Processing helix chain 'T' and resid 112 through 121 Processing helix chain 'T' and resid 123 through 144 Processing helix chain 'T' and resid 153 through 172 removed outlier: 3.683A pdb=" N ALA T 172 " --> pdb=" O ALA T 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 15 Processing helix chain 'U' and resid 20 through 47 removed outlier: 4.715A pdb=" N ASN U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA U 36 " --> pdb=" O ARG U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 64 through 69 Processing helix chain 'U' and resid 77 through 102 Processing helix chain 'U' and resid 104 through 111 Processing helix chain 'U' and resid 114 through 122 Processing helix chain 'U' and resid 125 through 140 removed outlier: 3.990A pdb=" N TYR U 129 " --> pdb=" O SER U 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 162 Processing helix chain 'V' and resid 3 through 16 removed outlier: 3.970A pdb=" N VAL V 8 " --> pdb=" O VAL V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 33 Processing helix chain 'V' and resid 33 through 47 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 64 through 67 Processing helix chain 'V' and resid 75 through 100 Processing helix chain 'V' and resid 102 through 108 Processing helix chain 'V' and resid 112 through 121 Processing helix chain 'V' and resid 123 through 144 Processing helix chain 'V' and resid 153 through 172 Processing helix chain 'W' and resid 3 through 16 Processing helix chain 'W' and resid 20 through 47 removed outlier: 4.520A pdb=" N ASN W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 64 through 68 Processing helix chain 'W' and resid 77 through 102 Processing helix chain 'W' and resid 104 through 111 Processing helix chain 'W' and resid 114 through 122 Processing helix chain 'W' and resid 125 through 140 removed outlier: 3.998A pdb=" N TYR W 129 " --> pdb=" O SER W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 162 Processing helix chain 'X' and resid 3 through 16 removed outlier: 3.835A pdb=" N VAL X 8 " --> pdb=" O VAL X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 33 Processing helix chain 'X' and resid 33 through 47 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 64 through 67 Processing helix chain 'X' and resid 75 through 100 Processing helix chain 'X' and resid 102 through 109 Processing helix chain 'X' and resid 112 through 121 Processing helix chain 'X' and resid 123 through 143 Processing helix chain 'X' and resid 153 through 172 removed outlier: 3.574A pdb=" N VAL X 171 " --> pdb=" O ALA X 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'b' and resid 28 through 44 Processing helix chain 'b' and resid 50 through 54 Processing helix chain 'b' and resid 55 through 64 Processing helix chain 'b' and resid 68 through 79 Processing helix chain 'b' and resid 79 through 87 Processing helix chain 'b' and resid 91 through 105 Processing helix chain 'b' and resid 110 through 125 removed outlier: 3.835A pdb=" N VAL b 114 " --> pdb=" O SER b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 135 removed outlier: 3.528A pdb=" N TYR b 133 " --> pdb=" O ASP b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 136 through 143 Processing helix chain 'b' and resid 160 through 171 removed outlier: 3.921A pdb=" N PHE b 164 " --> pdb=" O ARG b 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR b 165 " --> pdb=" O THR b 161 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE b 168 " --> pdb=" O PHE b 164 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 196 Processing helix chain 'c' and resid 250 through 263 removed outlier: 4.379A pdb=" N SER c 254 " --> pdb=" O TYR c 250 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA c 255 " --> pdb=" O ASP c 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 243 through 249 removed outlier: 6.540A pdb=" N ILE c 228 " --> pdb=" O VAL c 267 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL c 267 " --> pdb=" O ILE c 228 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 4062 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: 13.39 Time building geometry restraints manager: 37.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17043 1.03 - 1.23: 178 1.23 - 1.42: 7803 1.42 - 1.62: 10434 1.62 - 1.81: 104 Bond restraints: 35562 Sorted by residual: bond pdb=" ND2 MEN N 72 " pdb=" HD2 MEN N 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" ND2 MEN V 72 " pdb=" HD2 MEN V 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" N MEN T 72 " pdb=" H MEN T 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" ND2 MEN X 72 " pdb=" HD2 MEN X 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" ND2 MEN R 72 " pdb=" HD2 MEN R 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.02e+01 ... (remaining 35557 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.47: 252 105.47 - 113.44: 40434 113.44 - 121.40: 16199 121.40 - 129.37: 6641 129.37 - 137.33: 83 Bond angle restraints: 63609 Sorted by residual: angle pdb=" C1B CYC X 201 " pdb=" CHB CYC X 201 " pdb=" C4A CYC X 201 " ideal model delta sigma weight residual 126.10 137.33 -11.23 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLN N 65 " pdb=" CB GLN N 65 " pdb=" CG GLN N 65 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.01e+01 angle pdb=" C1B CYC R 202 " pdb=" CHB CYC R 202 " pdb=" C4A CYC R 202 " ideal model delta sigma weight residual 126.10 135.65 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C4C CYC W 201 " pdb=" C3C CYC W 201 " pdb=" CAC CYC W 201 " ideal model delta sigma weight residual 113.00 122.05 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C4C CYC U 201 " pdb=" C3C CYC U 201 " pdb=" CAC CYC U 201 " ideal model delta sigma weight residual 113.00 121.98 -8.98 3.00e+00 1.11e-01 8.95e+00 ... (remaining 63604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15393 17.90 - 35.80: 1241 35.80 - 53.71: 374 53.71 - 71.61: 139 71.61 - 89.51: 26 Dihedral angle restraints: 17173 sinusoidal: 9665 harmonic: 7508 Sorted by residual: dihedral pdb=" CA GLU b 145 " pdb=" C GLU b 145 " pdb=" N ASN b 146 " pdb=" CA ASN b 146 " ideal model delta harmonic sigma weight residual 180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLN M 33 " pdb=" C GLN M 33 " pdb=" N ALA M 34 " pdb=" CA ALA M 34 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLN Q 33 " pdb=" C GLN Q 33 " pdb=" N ALA Q 34 " pdb=" CA ALA Q 34 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 17170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2537 0.069 - 0.138: 193 0.138 - 0.208: 10 0.208 - 0.277: 1 0.277 - 0.346: 5 Chirality restraints: 2746 Sorted by residual: chirality pdb=" C3C CYC U 201 " pdb=" C2C CYC U 201 " pdb=" C4C CYC U 201 " pdb=" CAC CYC U 201 " both_signs ideal model delta sigma weight residual False 2.62 2.27 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3C CYC W 201 " pdb=" C2C CYC W 201 " pdb=" C4C CYC W 201 " pdb=" CAC CYC W 201 " both_signs ideal model delta sigma weight residual False 2.62 2.28 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3C CYC Q 201 " pdb=" C2C CYC Q 201 " pdb=" C4C CYC Q 201 " pdb=" CAC CYC Q 201 " both_signs ideal model delta sigma weight residual False 2.62 2.29 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 2743 not shown) Planarity restraints: 5517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYC U 201 " 0.008 2.00e-02 2.50e+03 1.06e-01 2.53e+02 pdb=" OB CYC U 201 " -0.048 2.00e-02 2.50e+03 pdb=" C1B CYC U 201 " 0.024 2.00e-02 2.50e+03 pdb=" C2B CYC U 201 " -0.062 2.00e-02 2.50e+03 pdb=" C3B CYC U 201 " -0.107 2.00e-02 2.50e+03 pdb=" C4B CYC U 201 " -0.055 2.00e-02 2.50e+03 pdb=" CAB CYC U 201 " 0.224 2.00e-02 2.50e+03 pdb=" CHB CYC U 201 " 0.129 2.00e-02 2.50e+03 pdb=" CMB CYC U 201 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC Q 201 " 0.003 2.00e-02 2.50e+03 1.05e-01 2.46e+02 pdb=" OB CYC Q 201 " -0.042 2.00e-02 2.50e+03 pdb=" C1B CYC Q 201 " 0.023 2.00e-02 2.50e+03 pdb=" C2B CYC Q 201 " -0.059 2.00e-02 2.50e+03 pdb=" C3B CYC Q 201 " -0.106 2.00e-02 2.50e+03 pdb=" C4B CYC Q 201 " -0.057 2.00e-02 2.50e+03 pdb=" CAB CYC Q 201 " 0.220 2.00e-02 2.50e+03 pdb=" CHB CYC Q 201 " 0.131 2.00e-02 2.50e+03 pdb=" CMB CYC Q 201 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC M 201 " 0.001 2.00e-02 2.50e+03 1.00e-01 2.26e+02 pdb=" OB CYC M 201 " 0.038 2.00e-02 2.50e+03 pdb=" C1B CYC M 201 " -0.019 2.00e-02 2.50e+03 pdb=" C2B CYC M 201 " 0.056 2.00e-02 2.50e+03 pdb=" C3B CYC M 201 " 0.101 2.00e-02 2.50e+03 pdb=" C4B CYC M 201 " 0.055 2.00e-02 2.50e+03 pdb=" CAB CYC M 201 " -0.210 2.00e-02 2.50e+03 pdb=" CHB CYC M 201 " -0.128 2.00e-02 2.50e+03 pdb=" CMB CYC M 201 " 0.107 2.00e-02 2.50e+03 ... (remaining 5514 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 3380 2.23 - 2.82: 79924 2.82 - 3.41: 113008 3.41 - 4.01: 154689 4.01 - 4.60: 234356 Nonbonded interactions: 585357 Sorted by model distance: nonbonded pdb="HH22 ARG S 79 " pdb=" O2D CYC S 201 " model vdw 1.633 1.850 nonbonded pdb="HH22 ARG O 79 " pdb=" O2D CYC O 201 " model vdw 1.636 1.850 nonbonded pdb="HH22 ARG U 79 " pdb=" O2D CYC U 201 " model vdw 1.653 1.850 nonbonded pdb="HH22 ARG M 79 " pdb=" O2D CYC M 201 " model vdw 1.667 1.850 nonbonded pdb="HH22 ARG Q 79 " pdb=" O2D CYC Q 201 " model vdw 1.678 1.850 ... (remaining 585352 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 'M' and (resid 1 through 46 or resid 48 through 162 or resid 201)) selection = (chain 'O' and (resid 1 through 46 or resid 48 through 162 or resid 201)) selection = (chain 'Q' and (resid 1 through 46 or resid 48 through 162 or resid 201)) selection = (chain 'S' and (resid 1 through 46 or resid 48 through 162 or resid 201)) selection = (chain 'U' and (resid 1 through 46 or resid 48 through 162 or resid 201)) selection = (chain 'W' and (resid 1 through 46 or resid 48 through 162 or resid 201)) } ncs_group { reference = (chain 'N' and (resid 1 through 85 or resid 87 through 172 or resid 201 through \ 202)) selection = (chain 'P' and (resid 1 through 85 or resid 87 through 172 or resid 201 through \ 202)) selection = (chain 'R' and (resid 1 through 85 or resid 87 through 172 or resid 201 through \ 202)) selection = (chain 'T' and (resid 1 through 85 or resid 87 through 172 or resid 201 through \ 202)) selection = (chain 'V' and (resid 1 through 85 or resid 87 through 172 or resid 201 through \ 202)) selection = (chain 'X' and (resid 1 through 85 or resid 87 through 172 or resid 201 through \ 202)) } 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: 7.390 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: 0.890 Extract box with map and model: 1.440 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 128.580 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.160 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.005 0.059 18471 Z= 0.357 Angle : 0.703 11.233 25122 Z= 0.324 Chirality : 0.039 0.346 2746 Planarity : 0.009 0.124 3292 Dihedral : 14.676 89.510 7176 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.23 % Allowed : 5.49 % Favored : 94.28 % 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: 2.76 (0.17), residues: 2250 helix: 2.23 (0.12), residues: 1770 sheet: 2.13 (1.03), residues: 14 loop : 0.34 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 128 HIS 0.004 0.002 HIS W 140 PHE 0.016 0.002 PHE b 168 TYR 0.011 0.002 TYR b 15 ARG 0.015 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 2.889 Fit side-chains revert: symmetry clash REVERT: Q 162 SER cc_start: 0.7285 (m) cc_final: 0.7081 (p) REVERT: W 39 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7502 (tm-30) outliers start: 4 outliers final: 3 residues processed: 236 average time/residue: 4.3045 time to fit residues: 1103.8596 Evaluate side-chains 231 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain c residue 218 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN O 68 GLN Q 68 GLN Q 139 ASN R 132 GLN T 68 GLN U 68 GLN W 70 GLN c 263 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18471 Z= 0.182 Angle : 0.581 7.043 25122 Z= 0.301 Chirality : 0.036 0.144 2746 Planarity : 0.004 0.050 3292 Dihedral : 9.760 76.844 3369 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.23 % Allowed : 5.09 % Favored : 94.68 % 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: 2.95 (0.17), residues: 2250 helix: 2.38 (0.12), residues: 1777 sheet: 2.00 (1.02), residues: 14 loop : 0.30 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 128 HIS 0.004 0.002 HIS W 140 PHE 0.019 0.002 PHE b 168 TYR 0.013 0.002 TYR W 135 ARG 0.007 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 3.168 Fit side-chains REVERT: Q 7 GLU cc_start: 0.7369 (tt0) cc_final: 0.7127 (tt0) REVERT: W 39 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7446 (tm-30) outliers start: 4 outliers final: 2 residues processed: 229 average time/residue: 4.1576 time to fit residues: 1037.2720 Evaluate side-chains 230 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN O 68 GLN Q 68 GLN R 132 GLN U 68 GLN W 70 GLN c 263 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18471 Z= 0.253 Angle : 0.660 7.429 25122 Z= 0.343 Chirality : 0.038 0.146 2746 Planarity : 0.005 0.064 3292 Dihedral : 9.945 75.618 3368 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.28 % Allowed : 4.92 % Favored : 94.79 % 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: 2.42 (0.17), residues: 2250 helix: 1.98 (0.11), residues: 1777 sheet: 2.00 (1.00), residues: 14 loop : 0.22 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 128 HIS 0.004 0.002 HIS W 140 PHE 0.024 0.002 PHE b 168 TYR 0.017 0.002 TYR b 15 ARG 0.006 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 228 time to evaluate : 3.010 Fit side-chains REVERT: M 117 GLU cc_start: 0.7420 (mp0) cc_final: 0.7185 (mp0) REVERT: V 79 MET cc_start: 0.8872 (tpp) cc_final: 0.8570 (tpp) outliers start: 5 outliers final: 4 residues processed: 232 average time/residue: 4.1528 time to fit residues: 1051.6133 Evaluate side-chains 235 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN O 39 GLN O 49 GLN O 68 GLN U 68 GLN ** W 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18471 Z= 0.140 Angle : 0.520 6.919 25122 Z= 0.269 Chirality : 0.034 0.142 2746 Planarity : 0.004 0.057 3292 Dihedral : 9.525 75.296 3368 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % 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: 2.98 (0.17), residues: 2250 helix: 2.41 (0.12), residues: 1777 sheet: 1.44 (0.92), residues: 18 loop : 0.27 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP b 211 HIS 0.004 0.002 HIS W 140 PHE 0.013 0.001 PHE b 168 TYR 0.010 0.001 TYR X 92 ARG 0.010 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 229 time to evaluate : 2.972 Fit side-chains REVERT: Q 7 GLU cc_start: 0.7320 (tt0) cc_final: 0.7053 (tt0) REVERT: Q 162 SER cc_start: 0.7281 (m) cc_final: 0.7077 (p) REVERT: V 79 MET cc_start: 0.8849 (tpp) cc_final: 0.8524 (tpp) REVERT: W 39 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7439 (tm-30) REVERT: b 167 MET cc_start: 0.6549 (tpp) cc_final: 0.6233 (tpp) outliers start: 3 outliers final: 2 residues processed: 230 average time/residue: 4.2445 time to fit residues: 1063.6305 Evaluate side-chains 232 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 68 GLN R 132 GLN S 35 ASN ** W 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18471 Z= 0.231 Angle : 0.639 7.436 25122 Z= 0.330 Chirality : 0.037 0.145 2746 Planarity : 0.005 0.068 3292 Dihedral : 9.894 76.084 3367 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.28 % Allowed : 5.04 % Favored : 94.68 % 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: 2.51 (0.17), residues: 2250 helix: 2.05 (0.11), residues: 1777 sheet: 1.54 (0.86), residues: 18 loop : 0.24 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 128 HIS 0.005 0.002 HIS W 140 PHE 0.023 0.002 PHE b 168 TYR 0.016 0.002 TYR b 15 ARG 0.009 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 238 time to evaluate : 2.923 Fit side-chains revert: symmetry clash REVERT: V 79 MET cc_start: 0.8867 (tpp) cc_final: 0.8508 (tpp) outliers start: 5 outliers final: 4 residues processed: 240 average time/residue: 4.1486 time to fit residues: 1086.9845 Evaluate side-chains 237 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 15 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 49 GLN O 68 GLN W 70 GLN c 263 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18471 Z= 0.221 Angle : 0.621 7.003 25122 Z= 0.321 Chirality : 0.036 0.145 2746 Planarity : 0.005 0.065 3292 Dihedral : 9.829 75.706 3367 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.28 % Allowed : 4.87 % Favored : 94.85 % 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: 2.49 (0.17), residues: 2250 helix: 2.03 (0.11), residues: 1777 sheet: 1.54 (0.85), residues: 18 loop : 0.22 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 128 HIS 0.005 0.002 HIS W 140 PHE 0.021 0.002 PHE b 168 TYR 0.014 0.002 TYR b 15 ARG 0.011 0.001 ARG T 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 2.856 Fit side-chains revert: symmetry clash REVERT: V 79 MET cc_start: 0.8889 (tpp) cc_final: 0.8516 (tpp) outliers start: 5 outliers final: 4 residues processed: 236 average time/residue: 4.1579 time to fit residues: 1075.9056 Evaluate side-chains 236 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 15 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 68 GLN ** W 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18471 Z= 0.249 Angle : 0.651 7.367 25122 Z= 0.337 Chirality : 0.037 0.147 2746 Planarity : 0.005 0.067 3292 Dihedral : 9.908 76.398 3367 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.28 % Allowed : 4.98 % Favored : 94.74 % 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: 2.38 (0.16), residues: 2250 helix: 1.95 (0.11), residues: 1777 sheet: 1.64 (0.85), residues: 18 loop : 0.22 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 128 HIS 0.004 0.002 HIS W 140 PHE 0.023 0.002 PHE b 168 TYR 0.016 0.002 TYR b 15 ARG 0.010 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 3.049 Fit side-chains revert: symmetry clash REVERT: V 79 MET cc_start: 0.8893 (tpp) cc_final: 0.8508 (tpp) outliers start: 5 outliers final: 4 residues processed: 235 average time/residue: 4.1521 time to fit residues: 1065.4441 Evaluate side-chains 237 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 15 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 49 GLN ** W 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18471 Z= 0.219 Angle : 0.623 7.112 25122 Z= 0.322 Chirality : 0.037 0.145 2746 Planarity : 0.005 0.068 3292 Dihedral : 9.861 75.780 3367 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.34 % Allowed : 4.92 % Favored : 94.74 % 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: 2.43 (0.17), residues: 2250 helix: 1.99 (0.11), residues: 1777 sheet: 1.61 (0.85), residues: 18 loop : 0.21 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 128 HIS 0.005 0.002 HIS W 140 PHE 0.021 0.002 PHE b 168 TYR 0.015 0.002 TYR b 15 ARG 0.012 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 2.941 Fit side-chains revert: symmetry clash REVERT: V 79 MET cc_start: 0.8893 (tpp) cc_final: 0.8510 (tpp) REVERT: W 39 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7439 (tm-30) outliers start: 6 outliers final: 4 residues processed: 237 average time/residue: 4.1385 time to fit residues: 1070.7252 Evaluate side-chains 237 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 15 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18471 Z= 0.153 Angle : 0.540 6.837 25122 Z= 0.279 Chirality : 0.034 0.143 2746 Planarity : 0.004 0.084 3292 Dihedral : 9.584 75.628 3367 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.23 % Allowed : 5.15 % Favored : 94.62 % 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: 2.89 (0.17), residues: 2250 helix: 2.34 (0.12), residues: 1777 sheet: 1.49 (0.85), residues: 18 loop : 0.25 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 128 HIS 0.004 0.002 HIS S 140 PHE 0.014 0.001 PHE R 98 TYR 0.010 0.001 TYR b 15 ARG 0.011 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 2.917 Fit side-chains REVERT: Q 7 GLU cc_start: 0.7331 (tt0) cc_final: 0.7013 (tt0) REVERT: Q 162 SER cc_start: 0.7338 (m) cc_final: 0.7126 (p) REVERT: S 49 GLN cc_start: 0.7654 (tp40) cc_final: 0.7341 (pm20) REVERT: V 79 MET cc_start: 0.8857 (tpp) cc_final: 0.8601 (tpp) REVERT: W 39 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7449 (tm-30) outliers start: 4 outliers final: 3 residues processed: 237 average time/residue: 3.9899 time to fit residues: 1033.7576 Evaluate side-chains 236 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN W 70 GLN c 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18471 Z= 0.264 Angle : 0.670 7.552 25122 Z= 0.347 Chirality : 0.038 0.147 2746 Planarity : 0.005 0.081 3292 Dihedral : 9.940 76.085 3367 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.34 % Allowed : 5.09 % Favored : 94.57 % 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: 2.36 (0.16), residues: 2250 helix: 1.94 (0.11), residues: 1777 sheet: 1.68 (0.85), residues: 18 loop : 0.21 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 128 HIS 0.005 0.002 HIS W 140 PHE 0.025 0.002 PHE b 168 TYR 0.017 0.002 TYR b 15 ARG 0.012 0.001 ARG R 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 3.177 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 236 average time/residue: 4.0172 time to fit residues: 1035.1916 Evaluate side-chains 236 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 232 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain P residue 15 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 26 optimal weight: 0.0020 chunk 49 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN W 70 GLN c 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102613 restraints weight = 42977.045| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 0.34 r_work: 0.2925 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2634 rms_B_bonded: 3.17 restraints_weight: 0.1250 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18471 Z= 0.229 Angle : 0.633 7.171 25122 Z= 0.327 Chirality : 0.037 0.146 2746 Planarity : 0.005 0.082 3292 Dihedral : 9.864 76.053 3367 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.40 % Allowed : 5.15 % Favored : 94.45 % 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: 2.40 (0.17), residues: 2250 helix: 1.96 (0.11), residues: 1777 sheet: 1.77 (0.84), residues: 18 loop : 0.20 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 128 HIS 0.005 0.002 HIS W 140 PHE 0.021 0.002 PHE b 168 TYR 0.015 0.002 TYR b 15 ARG 0.010 0.001 ARG R 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16323.14 seconds wall clock time: 284 minutes 33.62 seconds (17073.62 seconds total)