Starting phenix.real_space_refine on Sun Jul 21 01:24:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/07_2024/8h9f_34565.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/07_2024/8h9f_34565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/07_2024/8h9f_34565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/07_2024/8h9f_34565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/07_2024/8h9f_34565.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/07_2024/8h9f_34565.cif" } resolution = 2.69 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= 0.023 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 P 5 5.49 5 S 63 5.16 5 C 8059 2.51 5 N 1938 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 3": "OD1" <-> "OD2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "5 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 38": "NH1" <-> "NH2" Residue "7 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 38": "NH1" <-> "NH2" Residue "8 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "M GLU 133": "OE1" <-> "OE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12265 Number of models: 1 Model: "" Number of chains: 22 Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "3" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Time building chain proxies: 9.40, per 1000 atoms: 0.77 Number of scatterers: 12265 At special positions: 0 Unit cell: (112.42, 104.39, 137.24, 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 63 16.00 P 5 15.00 O 2200 8.00 N 1938 7.00 C 8059 6.00 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=0, symmetry=0 Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.6 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 5 sheets defined 77.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain '1' and resid 2 through 15 Processing helix chain '1' and resid 17 through 39 removed outlier: 4.276A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 removed outlier: 3.516A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 removed outlier: 3.610A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 2 61 " --> pdb=" O SER 2 57 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 17 removed outlier: 4.040A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 removed outlier: 3.517A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 3 61 " --> pdb=" O SER 3 57 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 removed outlier: 3.850A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 17 through 39 removed outlier: 4.427A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.679A pdb=" N GLU 5 58 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 4.045A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 39 removed outlier: 4.428A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 17 through 39 removed outlier: 4.404A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.553A pdb=" N PHE 7 73 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.984A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 removed outlier: 3.550A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE 8 73 " --> pdb=" O PHE 8 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 49 removed outlier: 3.979A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.655A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 109 through 118 removed outlier: 3.690A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.552A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 187 through 193 removed outlier: 3.540A pdb=" N SER G 191 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.687A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.296A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.615A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 97 removed outlier: 3.891A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.524A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.645A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.641A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 85 removed outlier: 3.670A pdb=" N THR N 81 " --> pdb=" O ILE N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.881A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.003A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 138 removed outlier: 3.513A pdb=" N LEU N 137 " --> pdb=" O PRO N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 181 removed outlier: 3.559A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 153 - end of helix Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 4 through 9 Processing helix chain 'P' and resid 9 through 19 removed outlier: 3.598A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Proline residue: P 15 - end of helix removed outlier: 3.552A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'Q' and resid 1 through 7 removed outlier: 5.605A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 22 removed outlier: 3.533A pdb=" N MET Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.657A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.749A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 79 removed outlier: 4.387A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.694A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 93 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 3.861A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.113A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA G 127 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 5.216A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY H 80 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.286A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'N' and resid 13 through 14 949 hydrogen bonds defined for protein. 2788 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: 3.93 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1910 1.31 - 1.43: 3225 1.43 - 1.56: 7244 1.56 - 1.68: 11 1.68 - 1.81: 115 Bond restraints: 12505 Sorted by residual: bond pdb=" C ARG 2 38 " pdb=" O ARG 2 38 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.19e-02 7.06e+03 2.51e+01 bond pdb=" C ARG 3 38 " pdb=" CA AARG 3 38 " ideal model delta sigma weight residual 1.522 1.583 -0.061 1.37e-02 5.33e+03 1.98e+01 bond pdb=" C ARG 2 38 " pdb=" CA AARG 2 38 " ideal model delta sigma weight residual 1.524 1.580 -0.056 1.32e-02 5.74e+03 1.82e+01 bond pdb=" C31 3PH Q 101 " pdb=" O31 3PH Q 101 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C21 3PH Q 101 " pdb=" O21 3PH Q 101 " ideal model delta sigma weight residual 1.328 1.400 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 12500 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.15: 275 106.15 - 113.21: 6896 113.21 - 120.27: 4955 120.27 - 127.33: 4689 127.33 - 134.39: 92 Bond angle restraints: 16907 Sorted by residual: angle pdb=" O ARG 2 38 " pdb=" C ARG 2 38 " pdb=" CA BARG 2 38 " ideal model delta sigma weight residual 120.42 126.91 -6.49 1.06e+00 8.90e-01 3.75e+01 angle pdb=" O ARG 2 38 " pdb=" C ARG 2 38 " pdb=" CA AARG 2 38 " ideal model delta sigma weight residual 120.24 126.98 -6.74 1.11e+00 8.12e-01 3.68e+01 angle pdb=" C LEU N 137 " pdb=" N ILE N 138 " pdb=" CA ILE N 138 " ideal model delta sigma weight residual 120.24 123.89 -3.65 6.30e-01 2.52e+00 3.36e+01 angle pdb=" N ARG 2 38 " pdb=" CA BARG 2 38 " pdb=" C ARG 2 38 " ideal model delta sigma weight residual 111.36 117.11 -5.75 1.09e+00 8.42e-01 2.78e+01 angle pdb=" N SER G 121 " pdb=" CA SER G 121 " pdb=" C SER G 121 " ideal model delta sigma weight residual 113.43 106.80 6.63 1.26e+00 6.30e-01 2.77e+01 ... (remaining 16902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 7086 27.06 - 54.12: 288 54.12 - 81.18: 40 81.18 - 108.24: 2 108.24 - 135.30: 1 Dihedral angle restraints: 7417 sinusoidal: 2871 harmonic: 4546 Sorted by residual: dihedral pdb=" CD BARG 2 38 " pdb=" NE BARG 2 38 " pdb=" CZ BARG 2 38 " pdb=" NH1BARG 2 38 " ideal model delta sinusoidal sigma weight residual 0.00 -61.88 61.88 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA LEU H 145 " pdb=" C LEU H 145 " pdb=" N GLU H 146 " pdb=" CA GLU H 146 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA5 CDL R 101 " pdb=" CA4 CDL R 101 " pdb=" OA6 CDL R 101 " pdb=" CA6 CDL R 101 " ideal model delta sinusoidal sigma weight residual 168.24 -56.46 -135.30 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 7414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1407 0.042 - 0.085: 428 0.085 - 0.127: 121 0.127 - 0.169: 16 0.169 - 0.212: 6 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA ILE 4 71 " pdb=" N ILE 4 71 " pdb=" C ILE 4 71 " pdb=" CB ILE 4 71 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE P 5 " pdb=" N ILE P 5 " pdb=" C ILE P 5 " pdb=" CB ILE P 5 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA VAL H 77 " pdb=" N VAL H 77 " pdb=" C VAL H 77 " pdb=" CB VAL H 77 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1975 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG 2 38 " 0.962 9.50e-02 1.11e+02 4.31e-01 1.12e+02 pdb=" NE BARG 2 38 " -0.058 2.00e-02 2.50e+03 pdb=" CZ BARG 2 38 " -0.009 2.00e-02 2.50e+03 pdb=" NH1BARG 2 38 " 0.002 2.00e-02 2.50e+03 pdb=" NH2BARG 2 38 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 14 " 0.429 9.50e-02 1.11e+02 1.92e-01 2.26e+01 pdb=" NE ARG I 14 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG I 14 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG I 14 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 14 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 3 38 " 0.036 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" O ARG 3 38 " -0.014 2.00e-02 2.50e+03 pdb=" CA AARG 3 38 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN 3 39 " -0.012 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1151 2.74 - 3.28: 13035 3.28 - 3.82: 20859 3.82 - 4.36: 25655 4.36 - 4.90: 43674 Nonbonded interactions: 104374 Sorted by model distance: nonbonded pdb=" O ARG N 66 " pdb=" OG SER N 69 " model vdw 2.198 2.440 nonbonded pdb=" O LYS G 63 " pdb=" NZ LYS G 101 " model vdw 2.235 2.520 nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.263 2.520 nonbonded pdb=" NZ LYS Q 27 " pdb=" O32 3PH Q 101 " model vdw 2.302 2.520 nonbonded pdb=" O GLY G 114 " pdb=" NH1 ARG G 118 " model vdw 2.308 2.520 ... (remaining 104369 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 '1' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '2' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '3' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '4' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '5' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '6' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '7' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '8' and (resid 1 through 37 or resid 39 through 75)) } 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: 7.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.290 Process input model: 39.850 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 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:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.072 12505 Z= 0.337 Angle : 0.689 8.890 16907 Z= 0.404 Chirality : 0.045 0.212 1978 Planarity : 0.011 0.431 2080 Dihedral : 14.638 135.299 4517 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 (0.19), residues: 1560 helix: -1.16 (0.14), residues: 1115 sheet: -0.87 (0.54), residues: 88 loop : -2.48 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 10 HIS 0.004 0.001 HIS G 120 PHE 0.019 0.002 PHE 8 29 TYR 0.015 0.001 TYR I 12 ARG 0.003 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.300 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7614 (m-80) cc_final: 0.6829 (t80) REVERT: 5 75 MET cc_start: 0.4321 (mtp) cc_final: 0.3877 (mtt) REVERT: 6 7 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7635 (mttp) REVERT: 8 60 MET cc_start: 0.7882 (mmm) cc_final: 0.7360 (mmp) REVERT: G 64 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7394 (mmmt) REVERT: G 75 ARG cc_start: 0.7588 (mtp85) cc_final: 0.6779 (ptt180) REVERT: Q 28 MET cc_start: 0.8342 (mmp) cc_final: 0.7775 (mmp) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 1.1985 time to fit residues: 305.6918 Evaluate side-chains 205 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.0270 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 44 GLN G 120 HIS G 163 ASN H 15 GLN H 85 ASN H 111 ASN K 88 GLN M 136 ASN N 46 GLN N 47 GLN N 61 HIS N 101 ASN N 123 ASN N 172 HIS ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN S 75 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12505 Z= 0.177 Angle : 0.545 6.548 16907 Z= 0.290 Chirality : 0.041 0.168 1978 Planarity : 0.004 0.037 2080 Dihedral : 10.596 138.515 1842 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.63 % Allowed : 10.20 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.24 (0.21), residues: 1560 helix: 0.82 (0.15), residues: 1116 sheet: -0.66 (0.55), residues: 91 loop : -1.55 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 28 HIS 0.002 0.000 HIS H 51 PHE 0.023 0.001 PHE R 79 TYR 0.010 0.001 TYR G 44 ARG 0.003 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 1.289 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7485 (m-80) cc_final: 0.6732 (t80) REVERT: 5 60 MET cc_start: 0.7567 (mmm) cc_final: 0.7344 (mmt) REVERT: 5 75 MET cc_start: 0.3987 (mtp) cc_final: 0.3707 (mtt) REVERT: 6 7 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7610 (mttp) REVERT: 8 60 MET cc_start: 0.7540 (mmm) cc_final: 0.7338 (mmp) REVERT: G 64 LYS cc_start: 0.7843 (mmtt) cc_final: 0.7331 (mmmt) REVERT: G 75 ARG cc_start: 0.7551 (mtp85) cc_final: 0.6745 (ptt90) REVERT: G 195 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: H 32 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7511 (m-40) REVERT: H 68 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: I 7 GLN cc_start: 0.7429 (mm110) cc_final: 0.7186 (mt0) REVERT: N 199 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8431 (tt) outliers start: 32 outliers final: 8 residues processed: 239 average time/residue: 1.1977 time to fit residues: 311.0234 Evaluate side-chains 220 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 46 optimal weight: 0.0470 chunk 110 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12505 Z= 0.179 Angle : 0.518 7.795 16907 Z= 0.274 Chirality : 0.040 0.204 1978 Planarity : 0.004 0.037 2080 Dihedral : 10.085 141.636 1842 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.55 % Allowed : 13.71 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1560 helix: 1.58 (0.15), residues: 1115 sheet: -0.51 (0.55), residues: 91 loop : -1.10 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.022 0.001 PHE R 79 TYR 0.012 0.001 TYR I 12 ARG 0.002 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.453 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7460 (m-80) cc_final: 0.6740 (t80) REVERT: 5 75 MET cc_start: 0.4018 (mtp) cc_final: 0.3806 (mtt) REVERT: 6 7 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7632 (mttp) REVERT: G 35 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: G 64 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7292 (mmmt) REVERT: G 75 ARG cc_start: 0.7511 (mtp85) cc_final: 0.6650 (ptt180) REVERT: G 154 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: G 195 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7537 (m-30) outliers start: 31 outliers final: 6 residues processed: 229 average time/residue: 1.2187 time to fit residues: 303.1638 Evaluate side-chains 217 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12505 Z= 0.166 Angle : 0.504 8.039 16907 Z= 0.266 Chirality : 0.040 0.183 1978 Planarity : 0.003 0.038 2080 Dihedral : 9.750 143.133 1842 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.99 % Allowed : 15.70 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.22), residues: 1560 helix: 1.95 (0.16), residues: 1115 sheet: -0.47 (0.54), residues: 91 loop : -0.87 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.003 0.000 HIS H 51 PHE 0.025 0.001 PHE R 79 TYR 0.012 0.001 TYR G 193 ARG 0.003 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 1.399 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7436 (m-80) cc_final: 0.6745 (t80) REVERT: G 64 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7253 (mmmt) REVERT: G 75 ARG cc_start: 0.7508 (mtp85) cc_final: 0.6569 (ptt90) REVERT: G 154 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: N 181 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6874 (tpp) REVERT: N 199 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8409 (tt) REVERT: S 78 VAL cc_start: 0.7726 (t) cc_final: 0.7512 (t) outliers start: 24 outliers final: 7 residues processed: 219 average time/residue: 1.2535 time to fit residues: 298.0634 Evaluate side-chains 212 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 202 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12505 Z= 0.180 Angle : 0.511 8.162 16907 Z= 0.268 Chirality : 0.040 0.196 1978 Planarity : 0.003 0.038 2080 Dihedral : 9.515 144.184 1842 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.55 % Allowed : 15.94 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 2.00 (0.22), residues: 1560 helix: 2.09 (0.15), residues: 1116 sheet: -0.26 (0.54), residues: 91 loop : -0.73 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.024 0.001 PHE R 79 TYR 0.012 0.001 TYR T 32 ARG 0.002 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 1.445 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7384 (m-80) cc_final: 0.6726 (t80) REVERT: G 75 ARG cc_start: 0.7489 (mtp85) cc_final: 0.6537 (ptt90) REVERT: G 154 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: G 195 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: H 68 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: N 147 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7872 (mt) REVERT: N 199 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8382 (tt) REVERT: S 78 VAL cc_start: 0.7718 (t) cc_final: 0.7501 (t) REVERT: S 85 TRP cc_start: 0.8501 (OUTLIER) cc_final: 0.7074 (m-90) outliers start: 31 outliers final: 5 residues processed: 214 average time/residue: 1.1487 time to fit residues: 268.5894 Evaluate side-chains 207 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.8980 chunk 131 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.0020 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 163 ASN R 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12505 Z= 0.157 Angle : 0.500 9.082 16907 Z= 0.262 Chirality : 0.040 0.184 1978 Planarity : 0.003 0.038 2080 Dihedral : 9.254 145.148 1842 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.55 % Allowed : 16.41 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 2.17 (0.22), residues: 1560 helix: 2.19 (0.15), residues: 1122 sheet: -0.13 (0.55), residues: 91 loop : -0.64 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 10 HIS 0.002 0.000 HIS H 51 PHE 0.024 0.001 PHE R 79 TYR 0.010 0.001 TYR G 193 ARG 0.004 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.282 Fit side-chains REVERT: 1 66 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6313 (tmm) REVERT: 4 69 PHE cc_start: 0.7296 (m-80) cc_final: 0.6671 (t80) REVERT: G 75 ARG cc_start: 0.7495 (mtp85) cc_final: 0.6657 (ptt180) REVERT: G 154 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: G 195 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7420 (m-30) REVERT: N 163 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7828 (m-40) REVERT: N 199 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8406 (tt) REVERT: S 78 VAL cc_start: 0.7685 (t) cc_final: 0.7465 (t) REVERT: S 85 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.7045 (m-90) outliers start: 31 outliers final: 6 residues processed: 220 average time/residue: 1.1995 time to fit residues: 287.6207 Evaluate side-chains 206 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 194 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 106 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 88 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12505 Z= 0.153 Angle : 0.505 9.487 16907 Z= 0.263 Chirality : 0.040 0.188 1978 Planarity : 0.003 0.039 2080 Dihedral : 9.079 145.892 1842 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.23 % Allowed : 17.29 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 2.35 (0.22), residues: 1560 helix: 2.32 (0.15), residues: 1116 sheet: -0.03 (0.54), residues: 91 loop : -0.48 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 10 HIS 0.003 0.001 HIS N 168 PHE 0.024 0.001 PHE R 79 TYR 0.010 0.001 TYR G 193 ARG 0.004 0.000 ARG H 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 1.243 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7220 (m-80) cc_final: 0.6596 (t80) REVERT: G 75 ARG cc_start: 0.7511 (mtp85) cc_final: 0.6512 (ptt90) REVERT: G 154 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: G 195 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: S 85 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.6995 (m-90) outliers start: 27 outliers final: 9 residues processed: 212 average time/residue: 1.1548 time to fit residues: 266.5469 Evaluate side-chains 207 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.0030 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 0.0070 chunk 99 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN N 225 ASN R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12505 Z= 0.146 Angle : 0.506 9.968 16907 Z= 0.261 Chirality : 0.039 0.175 1978 Planarity : 0.003 0.039 2080 Dihedral : 8.945 146.346 1842 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.15 % Allowed : 17.53 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 2.48 (0.22), residues: 1560 helix: 2.40 (0.15), residues: 1116 sheet: -0.02 (0.55), residues: 89 loop : -0.41 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 10 HIS 0.002 0.000 HIS H 66 PHE 0.024 0.001 PHE R 79 TYR 0.009 0.001 TYR G 193 ARG 0.003 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: 1 66 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6308 (tmm) REVERT: 4 69 PHE cc_start: 0.7195 (m-80) cc_final: 0.6587 (t80) REVERT: G 75 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6468 (ptt90) REVERT: G 154 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7045 (mm-30) REVERT: G 195 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: I 32 LYS cc_start: 0.7564 (tttt) cc_final: 0.7353 (tttm) REVERT: S 85 TRP cc_start: 0.8500 (OUTLIER) cc_final: 0.6984 (m-90) outliers start: 26 outliers final: 10 residues processed: 218 average time/residue: 1.1926 time to fit residues: 283.2390 Evaluate side-chains 211 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 55 LYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN P 8 ASN R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12505 Z= 0.202 Angle : 0.530 11.315 16907 Z= 0.274 Chirality : 0.041 0.178 1978 Planarity : 0.003 0.040 2080 Dihedral : 9.018 146.928 1842 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.75 % Allowed : 18.25 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 (0.22), residues: 1560 helix: 2.37 (0.15), residues: 1109 sheet: 0.12 (0.56), residues: 89 loop : -0.47 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.023 0.001 PHE R 79 TYR 0.015 0.001 TYR I 12 ARG 0.003 0.000 ARG H 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 1.299 Fit side-chains REVERT: 1 66 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6372 (tmm) REVERT: 4 69 PHE cc_start: 0.7206 (m-80) cc_final: 0.6572 (t80) REVERT: G 75 ARG cc_start: 0.7466 (mtp85) cc_final: 0.6457 (ptt90) REVERT: G 154 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: G 195 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: I 37 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8360 (tmtt) REVERT: S 85 TRP cc_start: 0.8525 (OUTLIER) cc_final: 0.7021 (m-90) outliers start: 21 outliers final: 10 residues processed: 202 average time/residue: 1.2021 time to fit residues: 264.6949 Evaluate side-chains 210 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 92 optimal weight: 0.0060 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 0.0170 overall best weight: 0.5234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN N 163 ASN P 8 ASN R 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12505 Z= 0.162 Angle : 0.519 11.937 16907 Z= 0.268 Chirality : 0.040 0.171 1978 Planarity : 0.003 0.040 2080 Dihedral : 8.926 146.416 1842 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.35 % Allowed : 18.88 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 (0.22), residues: 1560 helix: 2.40 (0.15), residues: 1115 sheet: 0.14 (0.55), residues: 89 loop : -0.39 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 10 HIS 0.002 0.000 HIS H 51 PHE 0.023 0.001 PHE R 79 TYR 0.011 0.001 TYR M 149 ARG 0.003 0.000 ARG H 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.463 Fit side-chains REVERT: 1 66 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6378 (tmm) REVERT: 4 69 PHE cc_start: 0.7190 (m-80) cc_final: 0.6561 (t80) REVERT: G 75 ARG cc_start: 0.7469 (mtp85) cc_final: 0.6476 (ptt90) REVERT: G 123 GLN cc_start: 0.7421 (mt0) cc_final: 0.7125 (pt0) REVERT: G 154 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: G 195 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: I 37 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8356 (tmtt) REVERT: N 163 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7802 (m-40) REVERT: S 85 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.7001 (m-90) outliers start: 16 outliers final: 9 residues processed: 203 average time/residue: 1.2117 time to fit residues: 267.6877 Evaluate side-chains 206 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN N 163 ASN N 210 GLN P 8 ASN R 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108877 restraints weight = 20546.024| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.19 r_work: 0.3177 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 12505 Z= 0.212 Angle : 0.812 59.200 16907 Z= 0.481 Chirality : 0.040 0.199 1978 Planarity : 0.003 0.039 2080 Dihedral : 8.935 146.412 1842 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.43 % Allowed : 19.12 % Favored : 79.44 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.69 % 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 (0.22), residues: 1560 helix: 2.40 (0.15), residues: 1115 sheet: 0.14 (0.55), residues: 89 loop : -0.39 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 10 HIS 0.003 0.000 HIS H 51 PHE 0.023 0.001 PHE R 79 TYR 0.010 0.001 TYR I 12 ARG 0.003 0.000 ARG H 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5542.16 seconds wall clock time: 97 minutes 38.83 seconds (5858.83 seconds total)