Starting phenix.real_space_refine on Fri Mar 15 17:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/03_2024/8h9f_34565_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/03_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_34565/03_2024/8h9f_34565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/03_2024/8h9f_34565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/03_2024/8h9f_34565_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9f_34565/03_2024/8h9f_34565_updated.pdb" } 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-5265/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: 7.50, per 1000 atoms: 0.61 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: 4.69 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... running ksdssp... Secondary structure from input PDB file: 58 helices and 3 sheets defined 72.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain '1' and resid 3 through 38 removed outlier: 3.925A pdb=" N VAL 1 16 " --> pdb=" O GLY 1 12 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL 1 18 " --> pdb=" O ALA 1 14 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA 1 19 " --> pdb=" O THR 1 15 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY 1 20 " --> pdb=" O VAL 1 16 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 72 removed outlier: 3.721A pdb=" N LYS 1 43 " --> pdb=" O PRO 1 40 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLN 1 44 " --> pdb=" O SER 1 41 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU 1 46 " --> pdb=" O LYS 1 43 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU 1 58 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 38 removed outlier: 4.222A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL 2 18 " --> pdb=" O ALA 2 14 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA 2 19 " --> pdb=" O THR 2 15 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLY 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 72 removed outlier: 3.841A pdb=" N LYS 2 43 " --> pdb=" O PRO 2 40 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLN 2 44 " --> pdb=" O SER 2 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU 2 46 " --> pdb=" O LYS 2 43 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU 2 58 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 38 removed outlier: 4.040A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL 3 18 " --> pdb=" O ALA 3 14 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA 3 19 " --> pdb=" O THR 3 15 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY 3 20 " --> pdb=" O VAL 3 16 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 72 removed outlier: 3.551A pdb=" N LYS 3 43 " --> pdb=" O PRO 3 40 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLN 3 44 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU 3 46 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU 3 58 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 38 removed outlier: 4.212A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL 4 18 " --> pdb=" O ALA 4 14 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA 4 19 " --> pdb=" O THR 4 15 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY 4 20 " --> pdb=" O VAL 4 16 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 72 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 38 removed outlier: 4.211A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL 5 18 " --> pdb=" O ALA 5 14 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA 5 19 " --> pdb=" O THR 5 15 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLY 5 20 " --> pdb=" O VAL 5 16 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 72 removed outlier: 3.714A pdb=" N LYS 5 43 " --> pdb=" O PRO 5 40 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN 5 44 " --> pdb=" O SER 5 41 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU 5 46 " --> pdb=" O LYS 5 43 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER 5 57 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU 5 58 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 38 removed outlier: 4.045A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL 6 18 " --> pdb=" O ALA 6 14 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA 6 19 " --> pdb=" O THR 6 15 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY 6 20 " --> pdb=" O VAL 6 16 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 72 Processing helix chain '7' and resid 2 through 38 removed outlier: 4.231A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL 7 18 " --> pdb=" O ALA 7 14 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA 7 19 " --> pdb=" O THR 7 15 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY 7 20 " --> pdb=" O VAL 7 16 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 40 through 72 removed outlier: 4.898A pdb=" N GLN 7 44 " --> pdb=" O SER 7 41 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU 7 46 " --> pdb=" O LYS 7 43 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU 7 58 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU 7 72 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 38 removed outlier: 3.984A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL 8 18 " --> pdb=" O ALA 8 14 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA 8 19 " --> pdb=" O THR 8 15 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY 8 20 " --> pdb=" O VAL 8 16 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 40 through 72 removed outlier: 3.711A pdb=" N LYS 8 43 " --> pdb=" O PRO 8 40 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN 8 44 " --> pdb=" O SER 8 41 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU 8 58 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU 8 72 " --> pdb=" O PHE 8 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 48 removed outlier: 3.979A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.628A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 117 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 188 through 192 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) No H-bonds generated for 'chain 'G' and resid 188 through 192' Processing helix chain 'G' and resid 198 through 220 Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 121 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 29 through 38 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 29 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 47 Processing helix chain 'K' and resid 55 through 96 Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 132 through 138 Processing helix chain 'M' and resid 140 through 142 No H-bonds generated for 'chain 'M' and resid 140 through 142' Processing helix chain 'N' and resid 7 through 9 No H-bonds generated for 'chain 'N' and resid 7 through 9' Processing helix chain 'N' and resid 19 through 30 Proline residue: N 27 - end of helix removed outlier: 3.965A pdb=" N LEU N 30 " --> pdb=" O PHE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 58 Processing helix chain 'N' and resid 63 through 86 removed outlier: 3.636A pdb=" N THR N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP N 68 " --> pdb=" O LYS N 64 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER N 69 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU N 70 " --> pdb=" O ARG N 66 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N MET N 71 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR N 81 " --> pdb=" O ILE N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 98 through 118 Proline residue: N 107 - end of helix Processing helix chain 'N' and resid 121 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 135 through 182 Proline residue: N 139 - end of helix removed outlier: 4.222A pdb=" N ILE N 144 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU N 145 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR N 146 " --> pdb=" O ILE N 143 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN N 152 " --> pdb=" O LEU N 149 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.561A pdb=" N VAL N 158 " --> pdb=" O ALA N 155 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA N 162 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR N 165 " --> pdb=" O ALA N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 225 removed outlier: 3.631A pdb=" N ASN N 225 " --> pdb=" O TYR N 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 8 No H-bonds generated for 'chain 'P' and resid 5 through 8' Processing helix chain 'P' and resid 10 through 18 Proline residue: P 15 - end of helix Processing helix chain 'P' and resid 22 through 40 Processing helix chain 'Q' and resid 6 through 21 removed outlier: 3.520A pdb=" N TRP Q 9 " --> pdb=" O THR Q 6 " (cutoff:3.500A) Proline residue: Q 10 - end of helix removed outlier: 4.511A pdb=" N THR Q 14 " --> pdb=" O THR Q 11 " (cutoff:3.500A) Proline residue: Q 15 - end of helix removed outlier: 4.192A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE Q 21 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 29 Processing helix chain 'R' and resid 26 through 31 Processing helix chain 'R' and resid 36 through 54 Processing helix chain 'R' and resid 63 through 78 removed outlier: 4.387A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 87 removed outlier: 4.389A pdb=" N HIS R 86 " --> pdb=" O LYS R 82 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU R 87 " --> pdb=" O HIS R 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 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 45 through 61 Processing helix chain 'S' and resid 63 through 66 Processing helix chain 'S' and resid 69 through 92 Processing helix chain 'T' and resid 9 through 44 Proline residue: T 35 - end of helix Processing sheet with id= A, 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: 7.155A pdb=" N VAL G 126 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 17 through 22 removed outlier: 4.321A pdb=" N GLY H 80 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.847A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 1990 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: 3.89 Time building geometry restraints manager: 5.04 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: 1193 2.74 - 3.28: 13073 3.28 - 3.82: 20705 3.82 - 4.36: 26005 4.36 - 4.90: 43726 Nonbonded interactions: 104702 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 SER P 4 " pdb=" N ASN P 8 " model vdw 2.304 2.520 ... (remaining 104697 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: 10.730 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: 0.020 Extract box with map and model: 27.710 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 36.570 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.650 ------------------------------------------------------------------------------- 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= 0.334 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 : 1.233 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: 1.2023 time to fit residues: 306.6810 Evaluate side-chains 205 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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: 0.0370 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1000 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= 0.189 Angle : 0.537 6.477 16907 Z= 0.289 Chirality : 0.040 0.169 1978 Planarity : 0.005 0.043 2080 Dihedral : 10.673 138.324 1842 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.23 % Allowed : 10.44 % Favored : 87.33 % 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: -0.89 (0.20), residues: 1560 helix: -0.24 (0.15), residues: 1156 sheet: -0.50 (0.55), residues: 88 loop : -1.37 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.003 0.000 HIS H 51 PHE 0.016 0.001 PHE H 45 TYR 0.011 0.001 TYR I 12 ARG 0.004 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 248 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.422 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7513 (m-80) cc_final: 0.6657 (t80) REVERT: 5 75 MET cc_start: 0.3998 (mtp) cc_final: 0.3706 (mtt) REVERT: 6 7 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7639 (mttp) REVERT: 8 60 MET cc_start: 0.7825 (mmm) cc_final: 0.7433 (mmp) REVERT: G 56 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: G 64 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7351 (mmmt) REVERT: G 75 ARG cc_start: 0.7568 (mtp85) cc_final: 0.6758 (ptt180) REVERT: H 32 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7559 (m-40) REVERT: N 199 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8419 (tt) REVERT: Q 28 MET cc_start: 0.8329 (mmp) cc_final: 0.7785 (mmp) outliers start: 27 outliers final: 7 residues processed: 228 average time/residue: 1.3448 time to fit residues: 332.1877 Evaluate side-chains 218 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 39 SER 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 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: 6.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8243 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12505 Z= 0.186 Angle : 0.515 6.662 16907 Z= 0.277 Chirality : 0.040 0.189 1978 Planarity : 0.005 0.039 2080 Dihedral : 10.122 141.089 1842 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.87 % Allowed : 12.83 % Favored : 84.30 % 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: -0.04 (0.21), residues: 1560 helix: 0.31 (0.15), residues: 1150 sheet: -0.29 (0.55), residues: 88 loop : -0.74 (0.35), residues: 322 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 0.016 0.001 PHE H 45 TYR 0.011 0.001 TYR I 12 ARG 0.003 0.000 ARG H 128 *********************** 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 243 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 1.216 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7450 (m-80) cc_final: 0.6660 (t80) REVERT: 6 7 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7638 (mttp) REVERT: 8 60 MET cc_start: 0.7791 (mmm) cc_final: 0.7471 (mmp) REVERT: G 56 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: G 64 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7309 (mmmt) REVERT: G 75 ARG cc_start: 0.7510 (mtp85) cc_final: 0.6657 (ptt90) REVERT: G 154 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: G 195 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: R 31 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6171 (tmt) outliers start: 35 outliers final: 10 residues processed: 223 average time/residue: 1.2630 time to fit residues: 304.8113 Evaluate side-chains 216 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 202 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 31 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: 0.7980 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 0.0030 chunk 137 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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: 0.8209 moved from start: 0.1605 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= 0.155 Angle : 0.495 7.190 16907 Z= 0.267 Chirality : 0.039 0.188 1978 Planarity : 0.005 0.036 2080 Dihedral : 9.772 143.183 1842 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.71 % Allowed : 13.94 % Favored : 83.35 % 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: 0.46 (0.22), residues: 1560 helix: 0.70 (0.16), residues: 1138 sheet: -0.07 (0.55), residues: 88 loop : -0.62 (0.35), residues: 334 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 0.019 0.001 PHE S 86 TYR 0.008 0.001 TYR I 12 ARG 0.002 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 241 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: 4 69 PHE cc_start: 0.7451 (m-80) cc_final: 0.6683 (t80) REVERT: 8 60 MET cc_start: 0.7735 (mmm) cc_final: 0.7359 (mmp) REVERT: G 64 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7246 (mmmt) REVERT: G 75 ARG cc_start: 0.7512 (mtp85) cc_final: 0.6635 (ptt180) REVERT: G 154 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: G 195 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: H 146 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5272 (mt-10) REVERT: N 199 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8381 (tt) REVERT: Q 28 MET cc_start: 0.8243 (mmp) cc_final: 0.7793 (mmp) REVERT: S 78 VAL cc_start: 0.7668 (t) cc_final: 0.7462 (t) outliers start: 33 outliers final: 13 residues processed: 220 average time/residue: 1.1678 time to fit residues: 279.5725 Evaluate side-chains 219 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 14 ILE 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 P residue 30 LEU 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: 0.0980 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 5 ASN R 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12505 Z= 0.203 Angle : 0.520 8.241 16907 Z= 0.277 Chirality : 0.041 0.208 1978 Planarity : 0.005 0.035 2080 Dihedral : 9.569 143.989 1842 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.19 % Allowed : 14.10 % Favored : 82.71 % 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: 0.59 (0.22), residues: 1560 helix: 0.80 (0.16), residues: 1138 sheet: -0.18 (0.54), residues: 90 loop : -0.53 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 PHE 0.017 0.001 PHE H 45 TYR 0.012 0.001 TYR I 12 ARG 0.004 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 238 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: 4 69 PHE cc_start: 0.7440 (m-80) cc_final: 0.6678 (t80) REVERT: 8 60 MET cc_start: 0.7754 (mmm) cc_final: 0.7363 (mmp) REVERT: G 35 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: G 56 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: G 75 ARG cc_start: 0.7498 (mtp85) cc_final: 0.6465 (ptt90) REVERT: G 154 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: G 195 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: N 199 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8396 (tt) REVERT: Q 28 MET cc_start: 0.8246 (mmp) cc_final: 0.7799 (mmp) REVERT: S 78 VAL cc_start: 0.7704 (t) cc_final: 0.7493 (t) REVERT: S 85 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7130 (m-90) outliers start: 39 outliers final: 15 residues processed: 213 average time/residue: 1.1583 time to fit residues: 267.8111 Evaluate side-chains 218 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER 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 35 GLU Chi-restraints excluded: chain G residue 56 ASP 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 H residue 73 SER Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 ILE 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 P residue 6 ILE Chi-restraints excluded: chain P residue 30 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: 2.9990 chunk 131 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 121 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 163 ASN N 225 ASN Q 5 ASN R 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12505 Z= 0.180 Angle : 0.506 8.376 16907 Z= 0.269 Chirality : 0.040 0.174 1978 Planarity : 0.005 0.034 2080 Dihedral : 9.327 144.717 1842 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.95 % Allowed : 15.14 % Favored : 81.91 % 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: 0.74 (0.22), residues: 1560 helix: 0.89 (0.16), residues: 1139 sheet: 0.02 (0.55), residues: 88 loop : -0.48 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 10 HIS 0.003 0.000 HIS H 51 PHE 0.016 0.001 PHE H 45 TYR 0.010 0.001 TYR I 12 ARG 0.002 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 236 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: 4 69 PHE cc_start: 0.7426 (m-80) cc_final: 0.6694 (t80) REVERT: 8 60 MET cc_start: 0.7734 (mmm) cc_final: 0.7345 (mmp) REVERT: G 35 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: G 75 ARG cc_start: 0.7520 (mtp85) cc_final: 0.6574 (ptt90) REVERT: G 154 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: G 195 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: H 32 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: N 147 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7742 (mt) REVERT: N 199 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8373 (tt) REVERT: S 78 VAL cc_start: 0.7662 (t) cc_final: 0.7449 (t) REVERT: S 85 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7108 (m-90) outliers start: 36 outliers final: 14 residues processed: 214 average time/residue: 1.2161 time to fit residues: 283.8260 Evaluate side-chains 214 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 5 residue 66 MET Chi-restraints excluded: chain 6 residue 66 MET 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 H residue 32 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 39 SER 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 N residue 206 VAL Chi-restraints excluded: chain P residue 30 LEU 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: 4.9990 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 Q 5 ASN R 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12505 Z= 0.200 Angle : 0.521 9.443 16907 Z= 0.276 Chirality : 0.040 0.164 1978 Planarity : 0.005 0.035 2080 Dihedral : 9.222 145.474 1842 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.71 % Allowed : 15.46 % Favored : 81.83 % 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: 0.81 (0.22), residues: 1560 helix: 0.94 (0.16), residues: 1138 sheet: 0.06 (0.55), residues: 88 loop : -0.43 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 10 HIS 0.003 0.000 HIS H 51 PHE 0.017 0.001 PHE H 45 TYR 0.011 0.001 TYR I 12 ARG 0.003 0.000 ARG G 133 *********************** 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 226 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: 4 69 PHE cc_start: 0.7411 (m-80) cc_final: 0.6647 (t80) REVERT: 8 60 MET cc_start: 0.7738 (mmm) cc_final: 0.7344 (mmp) REVERT: G 35 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: G 75 ARG cc_start: 0.7520 (mtp85) cc_final: 0.6555 (ptt90) REVERT: G 154 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: G 195 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: H 32 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7600 (m-40) REVERT: N 147 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7785 (mt) REVERT: N 199 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8370 (tt) REVERT: S 85 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.7055 (m-90) outliers start: 33 outliers final: 12 residues processed: 206 average time/residue: 1.2212 time to fit residues: 273.5155 Evaluate side-chains 210 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER 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 35 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 39 SER 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 R residue 31 MET 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: 1.9990 chunk 58 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12505 Z= 0.157 Angle : 0.508 9.878 16907 Z= 0.267 Chirality : 0.039 0.153 1978 Planarity : 0.005 0.035 2080 Dihedral : 9.044 146.314 1842 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.99 % Allowed : 16.18 % Favored : 81.83 % 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: 0.95 (0.22), residues: 1560 helix: 1.02 (0.16), residues: 1144 sheet: 0.26 (0.55), residues: 88 loop : -0.36 (0.35), residues: 328 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 0.014 0.001 PHE R 79 TYR 0.010 0.001 TYR T 32 ARG 0.001 0.000 ARG N 41 *********************** 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 222 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: 4 69 PHE cc_start: 0.7274 (m-80) cc_final: 0.6531 (t80) REVERT: 8 60 MET cc_start: 0.7706 (mmm) cc_final: 0.7333 (mmp) REVERT: G 35 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: G 75 ARG cc_start: 0.7528 (mtp85) cc_final: 0.6583 (ptt90) REVERT: G 123 GLN cc_start: 0.7380 (mt0) cc_final: 0.7117 (pt0) REVERT: G 154 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: G 195 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: N 147 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7735 (mt) REVERT: N 199 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8343 (tt) REVERT: S 85 TRP cc_start: 0.8507 (OUTLIER) cc_final: 0.7016 (m-90) outliers start: 24 outliers final: 11 residues processed: 207 average time/residue: 1.2086 time to fit residues: 271.6364 Evaluate side-chains 206 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 6 residue 66 MET 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 H residue 73 SER Chi-restraints excluded: chain I residue 36 GLU 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 R residue 31 MET 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: 0.8980 chunk 127 optimal weight: 0.0050 chunk 135 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 0.0050 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- 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 225 ASN Q 5 ASN R 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12505 Z= 0.156 Angle : 0.505 10.804 16907 Z= 0.266 Chirality : 0.039 0.156 1978 Planarity : 0.004 0.035 2080 Dihedral : 8.940 147.224 1842 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.07 % Allowed : 16.57 % Favored : 81.35 % 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: 1.07 (0.22), residues: 1560 helix: 1.10 (0.16), residues: 1144 sheet: 0.37 (0.56), residues: 86 loop : -0.29 (0.35), residues: 330 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 0.015 0.001 PHE R 79 TYR 0.010 0.001 TYR T 32 ARG 0.001 0.000 ARG G 133 *********************** 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 219 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 1.935 Fit side-chains revert: symmetry clash REVERT: 2 66 MET cc_start: 0.6877 (mtp) cc_final: 0.6625 (mtt) REVERT: 4 69 PHE cc_start: 0.7230 (m-80) cc_final: 0.6547 (t80) REVERT: 8 60 MET cc_start: 0.7677 (mmm) cc_final: 0.7382 (mmp) REVERT: G 35 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: G 68 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8421 (tp) REVERT: G 75 ARG cc_start: 0.7528 (mtp85) cc_final: 0.6610 (ptt90) REVERT: G 123 GLN cc_start: 0.7368 (mt0) cc_final: 0.7102 (pt0) REVERT: G 154 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: N 147 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7728 (mt) REVERT: N 199 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8355 (tt) REVERT: R 21 LYS cc_start: 0.6595 (mptt) cc_final: 0.6371 (mtmm) REVERT: S 85 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.6994 (m-90) outliers start: 25 outliers final: 10 residues processed: 204 average time/residue: 1.2911 time to fit residues: 286.6575 Evaluate side-chains 209 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER 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 35 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 36 GLU 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 R residue 31 MET 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: 0.8980 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN M 129 GLN N 163 ASN Q 5 ASN R 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2109 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 : 0.522 11.197 16907 Z= 0.272 Chirality : 0.040 0.310 1978 Planarity : 0.004 0.035 2080 Dihedral : 8.907 147.364 1842 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 16.81 % 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: 1.12 (0.22), residues: 1560 helix: 1.13 (0.16), residues: 1138 sheet: 0.37 (0.55), residues: 88 loop : -0.25 (0.35), residues: 334 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 0.017 0.001 PHE S 86 TYR 0.015 0.001 TYR G 193 ARG 0.001 0.000 ARG N 41 ********************** 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 219 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: 2 66 MET cc_start: 0.6895 (mtp) cc_final: 0.6645 (mtt) REVERT: 3 75 MET cc_start: 0.5473 (mtp) cc_final: 0.5264 (mtm) REVERT: 4 69 PHE cc_start: 0.7231 (m-80) cc_final: 0.6572 (t80) REVERT: 8 60 MET cc_start: 0.7672 (mmm) cc_final: 0.7363 (mmp) REVERT: G 35 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: G 75 ARG cc_start: 0.7532 (mtp85) cc_final: 0.6610 (ptt90) REVERT: G 123 GLN cc_start: 0.7379 (mt0) cc_final: 0.7121 (pt0) REVERT: G 154 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: N 147 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7738 (mt) REVERT: N 199 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8358 (tt) REVERT: R 21 LYS cc_start: 0.6582 (mptt) cc_final: 0.6243 (mtmt) REVERT: S 85 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.7032 (m-90) outliers start: 26 outliers final: 15 residues processed: 203 average time/residue: 1.2307 time to fit residues: 271.4345 Evaluate side-chains 206 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER 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 35 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 ILE 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 N residue 206 VAL Chi-restraints excluded: chain R residue 31 MET 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: 2.9990 chunk 110 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN N 4 ASN Q 5 ASN R 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108904 restraints weight = 20654.347| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.17 r_work: 0.3167 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 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 = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2071 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= 0.187 Angle : 0.529 11.213 16907 Z= 0.276 Chirality : 0.041 0.337 1978 Planarity : 0.005 0.035 2080 Dihedral : 8.932 147.601 1842 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.31 % Allowed : 16.97 % Favored : 80.72 % 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: 1.08 (0.22), residues: 1560 helix: 1.12 (0.16), residues: 1138 sheet: 0.25 (0.55), residues: 88 loop : -0.26 (0.35), residues: 334 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 0.015 0.001 PHE R 79 TYR 0.017 0.001 TYR G 193 ARG 0.001 0.000 ARG N 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.58 seconds wall clock time: 96 minutes 12.30 seconds (5772.30 seconds total)