Starting phenix.real_space_refine on Sun Aug 4 13:21:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnu_19395/08_2024/8rnu_19395.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnu_19395/08_2024/8rnu_19395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnu_19395/08_2024/8rnu_19395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnu_19395/08_2024/8rnu_19395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnu_19395/08_2024/8rnu_19395.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rnu_19395/08_2024/8rnu_19395.cif" } resolution = 3.4 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7044 2.51 5 N 1692 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 27": "OD1" <-> "OD2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 27": "OD1" <-> "OD2" Residue "K TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 16": "OE1" <-> "OE2" Residue "I ASP 27": "OD1" <-> "OD2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 27": "OD1" <-> "OD2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J GLU 14": "OE1" <-> "OE2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10848 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "E" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "I" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "G" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "B" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "D" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "J" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "F" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "L" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 904 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Time building chain proxies: 5.94, per 1000 atoms: 0.55 Number of scatterers: 10848 At special positions: 0 Unit cell: (114.48, 110.24, 68.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2064 8.00 N 1692 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS F 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 111 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS H 111 " distance=2.03 Simple disulfide: pdb=" SG CYS G 111 " - pdb=" SG CYS H 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 2.0 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 16 sheets defined 18.9% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 removed outlier: 3.982A pdb=" N ASN A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.230A pdb=" N LEU K 72 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 103 Processing helix chain 'K' and resid 104 through 111 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.524A pdb=" N ALA E 77 " --> pdb=" O ASN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'I' and resid 67 through 71 Processing helix chain 'I' and resid 74 through 78 Processing helix chain 'I' and resid 100 through 103 Processing helix chain 'I' and resid 104 through 111 Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.756A pdb=" N ASN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.017A pdb=" N LEU G 72 " --> pdb=" O LEU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 Processing helix chain 'G' and resid 104 through 111 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.745A pdb=" N ALA B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 73 through 78 removed outlier: 4.539A pdb=" N ALA H 77 " --> pdb=" O ILE H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 Processing helix chain 'H' and resid 104 through 111 Processing helix chain 'D' and resid 67 through 74 removed outlier: 3.888A pdb=" N ASN D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 100 through 103 removed outlier: 4.028A pdb=" N LEU D 103 " --> pdb=" O ILE D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 73 through 78 removed outlier: 4.550A pdb=" N ALA J 77 " --> pdb=" O ILE J 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY J 78 " --> pdb=" O ASN J 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 73 through 78' Processing helix chain 'J' and resid 100 through 103 Processing helix chain 'J' and resid 104 through 111 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 100 through 103 removed outlier: 3.504A pdb=" N LEU F 103 " --> pdb=" O ILE F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 100 through 103' Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 67 through 71 removed outlier: 3.602A pdb=" N GLU L 70 " --> pdb=" O ASN L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 103 Processing helix chain 'L' and resid 104 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 3.952A pdb=" N ASN A 6 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 15 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR A 44 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 53 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS A 52 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 118 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 95 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.799A pdb=" N ASP A 95 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A 115 " --> pdb=" O CYS B 52 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 54 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR A 117 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 46 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 15 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 10 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.529A pdb=" N LYS K 8 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL K 34 " --> pdb=" O ALA K 43 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA K 43 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP K 36 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU K 41 " --> pdb=" O ASP K 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 95 through 97 removed outlier: 3.740A pdb=" N THR K 116 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 10 removed outlier: 3.702A pdb=" N PHE E 10 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL E 15 " --> pdb=" O PHE E 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 95 through 96 removed outlier: 4.377A pdb=" N ASP E 95 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 118 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU E 115 " --> pdb=" O CYS F 52 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL F 54 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR E 117 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 15 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE F 10 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 16 through 19 removed outlier: 3.525A pdb=" N ASN I 32 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU I 45 " --> pdb=" O ASN I 32 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL I 34 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA I 43 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP I 36 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU I 41 " --> pdb=" O ASP I 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR I 42 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE I 55 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS I 52 " --> pdb=" O TYR J 117 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR J 116 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 95 through 96 removed outlier: 3.846A pdb=" N LEU J 41 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP J 36 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA J 43 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL J 34 " --> pdb=" O ALA J 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.732A pdb=" N PHE C 10 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 15 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 34 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 43 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 36 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 41 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 54 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 95 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.732A pdb=" N PHE C 10 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 15 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 51 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 54 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 95 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.864A pdb=" N ASP C 95 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR C 117 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR D 44 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 15 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN D 6 " --> pdb=" O SER D 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 8 through 9 removed outlier: 3.571A pdb=" N LYS G 8 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU G 45 " --> pdb=" O ASN G 32 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 34 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA G 43 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP G 36 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU G 41 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N CYS G 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP H 95 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 95 through 97 removed outlier: 3.653A pdb=" N ASP G 95 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR G 116 " --> pdb=" O ILE G 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP H 36 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 43 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS H 8 " --> pdb=" O PHE H 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 95 through 96 removed outlier: 4.406A pdb=" N ASP F 95 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 16 through 19 removed outlier: 3.504A pdb=" N ASN L 32 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU L 45 " --> pdb=" O ASN L 32 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL L 34 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 43 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP L 36 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU L 41 " --> pdb=" O ASP L 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 42 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE L 55 " --> pdb=" O THR L 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 95 through 97 removed outlier: 3.657A pdb=" N ASP L 95 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR L 116 " --> pdb=" O ILE L 97 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 711 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: 3.09 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.07: 2 1.07 - 1.26: 1897 1.26 - 1.44: 2658 1.44 - 1.63: 6430 1.63 - 1.81: 77 Bond restraints: 11064 Sorted by residual: bond pdb=" CG PRO I 64 " pdb=" CD PRO I 64 " ideal model delta sigma weight residual 1.503 0.886 0.617 3.40e-02 8.65e+02 3.30e+02 bond pdb=" CG PRO L 30 " pdb=" CD PRO L 30 " ideal model delta sigma weight residual 1.503 0.983 0.520 3.40e-02 8.65e+02 2.34e+02 bond pdb=" CG PRO E 21 " pdb=" CD PRO E 21 " ideal model delta sigma weight residual 1.503 1.164 0.339 3.40e-02 8.65e+02 9.96e+01 bond pdb=" N PRO I 64 " pdb=" CD PRO I 64 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.45e+01 bond pdb=" N PRO L 30 " pdb=" CD PRO L 30 " ideal model delta sigma weight residual 1.473 1.570 -0.097 1.40e-02 5.10e+03 4.78e+01 ... (remaining 11059 not shown) Histogram of bond angle deviations from ideal: 76.28 - 88.73: 5 88.73 - 101.19: 48 101.19 - 113.64: 6481 113.64 - 126.09: 8388 126.09 - 138.54: 102 Bond angle restraints: 15024 Sorted by residual: angle pdb=" N PRO L 30 " pdb=" CD PRO L 30 " pdb=" CG PRO L 30 " ideal model delta sigma weight residual 103.20 76.28 26.92 1.50e+00 4.44e-01 3.22e+02 angle pdb=" N PRO I 64 " pdb=" CD PRO I 64 " pdb=" CG PRO I 64 " ideal model delta sigma weight residual 103.20 76.91 26.29 1.50e+00 4.44e-01 3.07e+02 angle pdb=" CA PRO K 30 " pdb=" N PRO K 30 " pdb=" CD PRO K 30 " ideal model delta sigma weight residual 112.00 92.30 19.70 1.40e+00 5.10e-01 1.98e+02 angle pdb=" CA PRO E 21 " pdb=" N PRO E 21 " pdb=" CD PRO E 21 " ideal model delta sigma weight residual 112.00 94.08 17.92 1.40e+00 5.10e-01 1.64e+02 angle pdb=" N PRO E 21 " pdb=" CD PRO E 21 " pdb=" CG PRO E 21 " ideal model delta sigma weight residual 103.20 85.20 18.00 1.50e+00 4.44e-01 1.44e+02 ... (remaining 15019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5730 17.61 - 35.23: 778 35.23 - 52.84: 220 52.84 - 70.45: 35 70.45 - 88.07: 11 Dihedral angle restraints: 6774 sinusoidal: 2826 harmonic: 3948 Sorted by residual: dihedral pdb=" CA PRO L 23 " pdb=" C PRO L 23 " pdb=" N GLU L 24 " pdb=" CA GLU L 24 " ideal model delta harmonic sigma weight residual -180.00 -146.86 -33.14 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA PRO I 23 " pdb=" C PRO I 23 " pdb=" N GLU I 24 " pdb=" CA GLU I 24 " ideal model delta harmonic sigma weight residual -180.00 -147.56 -32.44 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA ILE B 100 " pdb=" C ILE B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta harmonic sigma weight residual -180.00 -148.28 -31.72 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 6771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1410 0.060 - 0.119: 307 0.119 - 0.179: 45 0.179 - 0.238: 1 0.238 - 0.298: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA PRO I 64 " pdb=" N PRO I 64 " pdb=" C PRO I 64 " pdb=" CB PRO I 64 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CG LEU I 72 " pdb=" CB LEU I 72 " pdb=" CD1 LEU I 72 " pdb=" CD2 LEU I 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CG LEU K 71 " pdb=" CB LEU K 71 " pdb=" CD1 LEU K 71 " pdb=" CD2 LEU K 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 1761 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP K 29 " -0.093 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO K 30 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO K 30 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO K 30 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 20 " 0.080 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO E 21 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO E 21 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 21 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 63 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO D 64 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.056 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 239 2.66 - 3.22: 10477 3.22 - 3.78: 17612 3.78 - 4.34: 23571 4.34 - 4.90: 36419 Nonbonded interactions: 88318 Sorted by model distance: nonbonded pdb=" NE2 GLN K 1 " pdb=" O VAL K 22 " model vdw 2.104 3.120 nonbonded pdb=" OG SER L 19 " pdb=" OD1 ASN L 32 " model vdw 2.136 3.040 nonbonded pdb=" ND2 ASN G 74 " pdb=" OG1 THR H 2 " model vdw 2.144 3.120 nonbonded pdb=" O ASP A 46 " pdb=" N ASP A 50 " model vdw 2.163 3.120 nonbonded pdb=" O ASN C 38 " pdb=" NH2 ARG G 66 " model vdw 2.170 3.120 ... (remaining 88313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.250 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.960 Find NCS groups from input model: 0.390 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3017 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 : 0.010 0.617 11064 Z= 0.664 Angle : 1.036 26.917 15024 Z= 0.602 Chirality : 0.050 0.298 1764 Planarity : 0.009 0.123 1920 Dihedral : 17.191 88.067 4164 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.32 % Allowed : 21.31 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 1272 helix: -0.79 (0.46), residues: 124 sheet: -0.34 (0.27), residues: 358 loop : -2.20 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 102 PHE 0.029 0.002 PHE J 25 TYR 0.009 0.001 TYR K 117 ARG 0.007 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.207 Fit side-chains REVERT: E 17 PHE cc_start: 0.4986 (t80) cc_final: 0.4681 (t80) REVERT: I 99 ASN cc_start: 0.7568 (t0) cc_final: 0.7287 (t0) REVERT: G 63 MET cc_start: 0.0841 (tmm) cc_final: 0.0368 (tmm) REVERT: B 17 PHE cc_start: 0.3153 (t80) cc_final: 0.2603 (t80) REVERT: F 63 MET cc_start: 0.2392 (tpt) cc_final: 0.0798 (tmm) REVERT: F 72 LEU cc_start: 0.6307 (mt) cc_final: 0.5652 (pp) outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 0.1660 time to fit residues: 15.1992 Evaluate side-chains 48 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN K 112 HIS ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 HIS ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN G 112 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS J 6 ASN J 112 HIS L 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3114 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 11064 Z= 0.294 Angle : 0.768 10.819 15024 Z= 0.404 Chirality : 0.051 0.167 1764 Planarity : 0.008 0.082 1920 Dihedral : 7.128 34.137 1406 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 3.61 % Allowed : 20.83 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.16 (0.22), residues: 1272 helix: -1.49 (0.40), residues: 134 sheet: -0.03 (0.28), residues: 342 loop : -2.20 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 102 PHE 0.022 0.002 PHE H 17 TYR 0.010 0.001 TYR E 108 ARG 0.008 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 50 time to evaluate : 1.296 Fit side-chains REVERT: A 50 ASP cc_start: 0.3312 (OUTLIER) cc_final: 0.2345 (m-30) REVERT: A 102 HIS cc_start: -0.3254 (OUTLIER) cc_final: -0.3843 (t-170) REVERT: E 21 PRO cc_start: 0.4382 (Cg_exo) cc_final: 0.3437 (Cg_endo) REVERT: E 50 ASP cc_start: 0.4424 (OUTLIER) cc_final: 0.1742 (m-30) REVERT: C 50 ASP cc_start: 0.5713 (OUTLIER) cc_final: 0.5364 (m-30) REVERT: C 102 HIS cc_start: -0.3795 (OUTLIER) cc_final: -0.4440 (t70) REVERT: G 63 MET cc_start: 0.1389 (tmm) cc_final: 0.0817 (tmm) REVERT: B 81 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7524 (mm) REVERT: F 45 LEU cc_start: -0.2154 (OUTLIER) cc_final: -0.6095 (pt) REVERT: F 63 MET cc_start: 0.2856 (tpt) cc_final: 0.0856 (tmm) REVERT: F 72 LEU cc_start: 0.6963 (mt) cc_final: 0.6294 (pp) outliers start: 45 outliers final: 16 residues processed: 91 average time/residue: 0.1635 time to fit residues: 24.3981 Evaluate side-chains 69 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 102 HIS Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain L residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 50.0000 chunk 33 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 106 optimal weight: 0.0870 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 96 optimal weight: 40.0000 overall best weight: 4.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 HIS ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN J 74 ASN F 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3047 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11064 Z= 0.229 Angle : 0.665 9.292 15024 Z= 0.351 Chirality : 0.049 0.155 1764 Planarity : 0.007 0.073 1920 Dihedral : 6.801 31.336 1406 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 4.97 % Allowed : 20.03 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.08 (0.23), residues: 1272 helix: -1.68 (0.38), residues: 140 sheet: -0.03 (0.27), residues: 352 loop : -2.08 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 102 PHE 0.025 0.001 PHE J 25 TYR 0.008 0.001 TYR E 53 ARG 0.005 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 46 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.2816 (OUTLIER) cc_final: 0.1899 (m-30) REVERT: A 102 HIS cc_start: -0.3222 (OUTLIER) cc_final: -0.3786 (t70) REVERT: K 91 MET cc_start: 0.1740 (pmm) cc_final: 0.0072 (mmp) REVERT: E 21 PRO cc_start: 0.4552 (Cg_exo) cc_final: 0.3723 (Cg_endo) REVERT: E 27 ASP cc_start: 0.0894 (OUTLIER) cc_final: -0.0776 (p0) REVERT: C 50 ASP cc_start: 0.5617 (OUTLIER) cc_final: 0.5308 (m-30) REVERT: C 102 HIS cc_start: -0.3655 (OUTLIER) cc_final: -0.4309 (t70) REVERT: G 63 MET cc_start: 0.1213 (tmm) cc_final: 0.0751 (tmm) REVERT: B 81 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7612 (mm) REVERT: D 101 ASP cc_start: 0.3595 (OUTLIER) cc_final: 0.3267 (m-30) REVERT: J 102 HIS cc_start: 0.0048 (OUTLIER) cc_final: -0.3558 (t70) REVERT: F 63 MET cc_start: 0.2196 (tpt) cc_final: 0.1092 (tmm) REVERT: F 72 LEU cc_start: 0.6951 (mt) cc_final: 0.6239 (pp) REVERT: L 63 MET cc_start: 0.0534 (tmm) cc_final: -0.0425 (tpt) outliers start: 62 outliers final: 29 residues processed: 104 average time/residue: 0.1821 time to fit residues: 29.7089 Evaluate side-chains 84 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 47 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 102 HIS Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 0.0980 chunk 106 optimal weight: 40.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3028 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11064 Z= 0.210 Angle : 0.639 9.774 15024 Z= 0.337 Chirality : 0.048 0.178 1764 Planarity : 0.007 0.070 1920 Dihedral : 6.494 29.177 1406 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.25 % Allowed : 21.07 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.23), residues: 1272 helix: -1.49 (0.39), residues: 140 sheet: -0.22 (0.27), residues: 374 loop : -2.00 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 112 PHE 0.026 0.001 PHE J 25 TYR 0.008 0.001 TYR B 80 ARG 0.004 0.001 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 48 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.2804 (OUTLIER) cc_final: 0.1919 (m-30) REVERT: A 102 HIS cc_start: -0.3117 (OUTLIER) cc_final: -0.3729 (t70) REVERT: K 91 MET cc_start: 0.1460 (pmm) cc_final: -0.0134 (mmp) REVERT: E 21 PRO cc_start: 0.4471 (Cg_exo) cc_final: 0.3717 (Cg_endo) REVERT: E 27 ASP cc_start: 0.1073 (OUTLIER) cc_final: -0.0579 (p0) REVERT: E 50 ASP cc_start: 0.4451 (OUTLIER) cc_final: 0.1982 (m-30) REVERT: C 50 ASP cc_start: 0.5725 (OUTLIER) cc_final: 0.5353 (m-30) REVERT: C 102 HIS cc_start: -0.3567 (OUTLIER) cc_final: -0.4119 (t70) REVERT: G 63 MET cc_start: 0.1257 (tmm) cc_final: 0.0821 (tmm) REVERT: G 102 HIS cc_start: -0.1795 (OUTLIER) cc_final: -0.3515 (t70) REVERT: B 81 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7818 (mm) REVERT: J 63 MET cc_start: -0.0244 (ppp) cc_final: -0.0473 (ppp) REVERT: F 63 MET cc_start: 0.2323 (tpt) cc_final: 0.1160 (tmm) REVERT: F 72 LEU cc_start: 0.7021 (mt) cc_final: 0.6282 (pp) REVERT: L 63 MET cc_start: 0.0750 (tmm) cc_final: -0.0080 (tpt) outliers start: 53 outliers final: 32 residues processed: 97 average time/residue: 0.1691 time to fit residues: 26.4936 Evaluate side-chains 85 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 45 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 102 HIS Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 50.0000 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3161 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11064 Z= 0.248 Angle : 0.684 9.550 15024 Z= 0.360 Chirality : 0.050 0.236 1764 Planarity : 0.007 0.068 1920 Dihedral : 6.658 29.433 1406 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 4.73 % Allowed : 21.55 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.23), residues: 1272 helix: -1.36 (0.42), residues: 126 sheet: -0.36 (0.27), residues: 374 loop : -2.04 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 102 PHE 0.027 0.002 PHE J 25 TYR 0.010 0.001 TYR E 108 ARG 0.004 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 47 time to evaluate : 1.259 Fit side-chains REVERT: A 50 ASP cc_start: 0.3031 (OUTLIER) cc_final: 0.1877 (m-30) REVERT: A 63 MET cc_start: 0.2613 (tpt) cc_final: 0.2410 (tpt) REVERT: A 102 HIS cc_start: -0.2884 (OUTLIER) cc_final: -0.3777 (t70) REVERT: K 91 MET cc_start: 0.1730 (pmm) cc_final: 0.0415 (mmp) REVERT: E 21 PRO cc_start: 0.4514 (Cg_exo) cc_final: 0.3776 (Cg_endo) REVERT: E 27 ASP cc_start: 0.1042 (OUTLIER) cc_final: -0.0130 (p0) REVERT: C 50 ASP cc_start: 0.5837 (OUTLIER) cc_final: 0.5556 (m-30) REVERT: C 102 HIS cc_start: -0.3570 (OUTLIER) cc_final: -0.4280 (t70) REVERT: G 63 MET cc_start: 0.1616 (tmm) cc_final: 0.1299 (tmm) REVERT: G 102 HIS cc_start: -0.1539 (OUTLIER) cc_final: -0.3476 (t70) REVERT: B 81 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7859 (mm) REVERT: D 63 MET cc_start: 0.3670 (tpp) cc_final: 0.3438 (tpp) REVERT: D 101 ASP cc_start: 0.3627 (OUTLIER) cc_final: 0.3310 (m-30) REVERT: J 63 MET cc_start: -0.0097 (ppp) cc_final: -0.0597 (ppp) REVERT: J 102 HIS cc_start: -0.0014 (OUTLIER) cc_final: -0.3670 (t70) REVERT: F 17 PHE cc_start: 0.2874 (m-80) cc_final: 0.2579 (m-80) REVERT: F 63 MET cc_start: 0.2217 (tpt) cc_final: 0.1174 (tmm) REVERT: L 102 HIS cc_start: 0.1175 (OUTLIER) cc_final: -0.0683 (t70) outliers start: 59 outliers final: 34 residues processed: 101 average time/residue: 0.1812 time to fit residues: 28.7502 Evaluate side-chains 90 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 46 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 102 HIS Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 74 optimal weight: 0.2980 chunk 31 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 106 optimal weight: 0.0970 chunk 59 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 123 optimal weight: 0.0020 overall best weight: 3.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 ASN ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3035 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11064 Z= 0.202 Angle : 0.637 11.517 15024 Z= 0.330 Chirality : 0.048 0.202 1764 Planarity : 0.007 0.068 1920 Dihedral : 6.344 27.491 1406 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.65 % Allowed : 20.99 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.23), residues: 1272 helix: -1.35 (0.40), residues: 140 sheet: -0.35 (0.27), residues: 374 loop : -2.01 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS F 102 PHE 0.028 0.001 PHE J 25 TYR 0.007 0.001 TYR I 117 ARG 0.004 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 51 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3341 (OUTLIER) cc_final: 0.2472 (m-30) REVERT: A 102 HIS cc_start: -0.3171 (OUTLIER) cc_final: -0.3813 (t70) REVERT: K 91 MET cc_start: 0.1817 (pmm) cc_final: 0.0532 (mmp) REVERT: K 102 HIS cc_start: -0.2140 (OUTLIER) cc_final: -0.4206 (t70) REVERT: E 21 PRO cc_start: 0.4855 (Cg_exo) cc_final: 0.4178 (Cg_endo) REVERT: E 27 ASP cc_start: 0.0264 (OUTLIER) cc_final: -0.0249 (p0) REVERT: E 50 ASP cc_start: 0.4403 (OUTLIER) cc_final: 0.1955 (m-30) REVERT: C 50 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.5550 (m-30) REVERT: C 102 HIS cc_start: -0.3698 (OUTLIER) cc_final: -0.4046 (t70) REVERT: G 63 MET cc_start: 0.1361 (tmm) cc_final: 0.1010 (tmm) REVERT: G 102 HIS cc_start: -0.1813 (OUTLIER) cc_final: -0.3645 (t70) REVERT: B 4 GLU cc_start: 0.6285 (pm20) cc_final: 0.5780 (mm-30) REVERT: B 81 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7973 (mm) REVERT: H 72 LEU cc_start: -0.2031 (tt) cc_final: -0.2427 (mt) REVERT: D 101 ASP cc_start: 0.3784 (OUTLIER) cc_final: 0.2878 (m-30) REVERT: J 18 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8780 (tp) REVERT: J 63 MET cc_start: -0.0294 (ppp) cc_final: -0.0826 (ppp) REVERT: J 102 HIS cc_start: -0.0015 (OUTLIER) cc_final: -0.3732 (t70) REVERT: F 17 PHE cc_start: 0.2847 (m-80) cc_final: 0.2579 (m-80) REVERT: F 63 MET cc_start: 0.2206 (tpt) cc_final: 0.1164 (tmm) REVERT: L 63 MET cc_start: 0.0725 (tmm) cc_final: -0.0301 (tpt) REVERT: L 102 HIS cc_start: 0.1055 (OUTLIER) cc_final: -0.0706 (t70) outliers start: 58 outliers final: 33 residues processed: 104 average time/residue: 0.1626 time to fit residues: 27.4951 Evaluate side-chains 96 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 50 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 40.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN C 1 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 HIS L 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3162 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11064 Z= 0.238 Angle : 0.680 13.831 15024 Z= 0.353 Chirality : 0.049 0.210 1764 Planarity : 0.007 0.068 1920 Dihedral : 6.520 28.644 1406 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 4.97 % Allowed : 21.23 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.23), residues: 1272 helix: -1.32 (0.42), residues: 128 sheet: -0.39 (0.27), residues: 374 loop : -2.00 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 112 PHE 0.027 0.002 PHE J 25 TYR 0.010 0.001 TYR F 80 ARG 0.005 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 51 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3165 (OUTLIER) cc_final: 0.1891 (m-30) REVERT: A 102 HIS cc_start: -0.3036 (OUTLIER) cc_final: -0.3894 (t70) REVERT: K 91 MET cc_start: 0.1376 (pmm) cc_final: 0.0665 (mmp) REVERT: K 102 HIS cc_start: -0.2121 (OUTLIER) cc_final: -0.4326 (t70) REVERT: E 21 PRO cc_start: 0.4881 (Cg_exo) cc_final: 0.4191 (Cg_endo) REVERT: E 27 ASP cc_start: 0.0992 (OUTLIER) cc_final: 0.0021 (p0) REVERT: C 50 ASP cc_start: 0.6060 (OUTLIER) cc_final: 0.5757 (m-30) REVERT: C 102 HIS cc_start: -0.3657 (OUTLIER) cc_final: -0.4210 (t70) REVERT: G 63 MET cc_start: 0.1746 (tmm) cc_final: 0.1297 (tmm) REVERT: G 102 HIS cc_start: -0.1573 (OUTLIER) cc_final: -0.3757 (t70) REVERT: B 17 PHE cc_start: 0.3262 (t80) cc_final: 0.2213 (t80) REVERT: B 81 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8029 (mm) REVERT: H 72 LEU cc_start: -0.2010 (tt) cc_final: -0.2437 (mt) REVERT: J 18 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8929 (tp) REVERT: J 63 MET cc_start: -0.0318 (ppp) cc_final: -0.0749 (ppp) REVERT: J 102 HIS cc_start: -0.0336 (OUTLIER) cc_final: -0.3750 (t70) REVERT: F 63 MET cc_start: 0.2196 (tpt) cc_final: 0.1182 (tmm) REVERT: L 102 HIS cc_start: 0.1201 (OUTLIER) cc_final: -0.0659 (t70) outliers start: 62 outliers final: 38 residues processed: 108 average time/residue: 0.1678 time to fit residues: 29.3305 Evaluate side-chains 99 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 50 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 40.0000 chunk 100 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3177 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11064 Z= 0.247 Angle : 0.687 12.818 15024 Z= 0.356 Chirality : 0.050 0.200 1764 Planarity : 0.007 0.071 1920 Dihedral : 6.578 29.002 1406 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.17 % Allowed : 22.04 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.23), residues: 1272 helix: -1.33 (0.42), residues: 128 sheet: -0.62 (0.26), residues: 386 loop : -1.99 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 35 PHE 0.026 0.002 PHE J 25 TYR 0.010 0.001 TYR F 80 ARG 0.004 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 48 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3000 (OUTLIER) cc_final: 0.1755 (m-30) REVERT: A 102 HIS cc_start: -0.2942 (OUTLIER) cc_final: -0.3914 (t70) REVERT: K 102 HIS cc_start: -0.2067 (OUTLIER) cc_final: -0.4284 (t70) REVERT: E 21 PRO cc_start: 0.4877 (Cg_exo) cc_final: 0.4145 (Cg_endo) REVERT: E 27 ASP cc_start: 0.0776 (OUTLIER) cc_final: 0.0020 (p0) REVERT: C 50 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.5863 (m-30) REVERT: C 102 HIS cc_start: -0.3627 (OUTLIER) cc_final: -0.4203 (t70) REVERT: G 63 MET cc_start: 0.1738 (tmm) cc_final: 0.1296 (tmm) REVERT: G 102 HIS cc_start: -0.1447 (OUTLIER) cc_final: -0.3827 (t70) REVERT: B 17 PHE cc_start: 0.3257 (t80) cc_final: 0.2262 (t80) REVERT: B 81 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7913 (mm) REVERT: D 100 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.3890 (mt) REVERT: D 101 ASP cc_start: 0.4054 (OUTLIER) cc_final: 0.3691 (m-30) REVERT: J 18 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8994 (tp) REVERT: J 63 MET cc_start: -0.0186 (ppp) cc_final: -0.0698 (ppp) REVERT: J 102 HIS cc_start: -0.0272 (OUTLIER) cc_final: -0.3799 (t70) REVERT: F 63 MET cc_start: 0.2131 (tpt) cc_final: 0.1134 (tmm) REVERT: L 102 HIS cc_start: 0.1443 (OUTLIER) cc_final: -0.0686 (t70) outliers start: 52 outliers final: 31 residues processed: 96 average time/residue: 0.1699 time to fit residues: 26.3746 Evaluate side-chains 92 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 48 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0070 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 50.0000 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 50.0000 chunk 112 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS K 35 HIS ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3107 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11064 Z= 0.214 Angle : 0.645 12.457 15024 Z= 0.334 Chirality : 0.049 0.196 1764 Planarity : 0.007 0.072 1920 Dihedral : 6.407 28.296 1406 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.61 % Allowed : 22.28 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.23), residues: 1272 helix: -1.43 (0.39), residues: 146 sheet: -0.50 (0.26), residues: 390 loop : -2.08 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 35 PHE 0.027 0.001 PHE J 25 TYR 0.008 0.001 TYR E 53 ARG 0.004 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 49 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.3292 (OUTLIER) cc_final: 0.2249 (m-30) REVERT: A 102 HIS cc_start: -0.3010 (OUTLIER) cc_final: -0.3833 (t70) REVERT: E 21 PRO cc_start: 0.4927 (Cg_exo) cc_final: 0.4253 (Cg_endo) REVERT: E 27 ASP cc_start: 0.0422 (OUTLIER) cc_final: -0.0077 (p0) REVERT: C 50 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5773 (m-30) REVERT: C 102 HIS cc_start: -0.3744 (OUTLIER) cc_final: -0.4163 (t70) REVERT: G 63 MET cc_start: 0.1507 (tmm) cc_final: 0.1097 (tmm) REVERT: G 102 HIS cc_start: -0.1118 (OUTLIER) cc_final: -0.3627 (t70) REVERT: B 17 PHE cc_start: 0.3608 (t80) cc_final: 0.2731 (t80) REVERT: B 81 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8027 (mm) REVERT: D 100 ILE cc_start: 0.3970 (OUTLIER) cc_final: 0.3667 (mt) REVERT: J 18 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8852 (tp) REVERT: J 63 MET cc_start: -0.0553 (ppp) cc_final: -0.1086 (ppp) REVERT: J 102 HIS cc_start: -0.0483 (OUTLIER) cc_final: -0.3886 (t70) REVERT: F 63 MET cc_start: 0.1810 (tpt) cc_final: 0.0852 (tmm) REVERT: L 102 HIS cc_start: 0.1385 (OUTLIER) cc_final: -0.0734 (t70) outliers start: 45 outliers final: 29 residues processed: 91 average time/residue: 0.1737 time to fit residues: 25.6489 Evaluate side-chains 88 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 48 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 40.0000 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN F 102 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3290 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11064 Z= 0.291 Angle : 0.753 12.447 15024 Z= 0.392 Chirality : 0.052 0.225 1764 Planarity : 0.007 0.069 1920 Dihedral : 6.897 30.706 1406 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.69 % Allowed : 22.12 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.28 (0.23), residues: 1272 helix: -1.41 (0.42), residues: 130 sheet: -0.43 (0.27), residues: 355 loop : -2.16 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 102 PHE 0.025 0.002 PHE J 25 TYR 0.014 0.001 TYR E 108 ARG 0.008 0.001 ARG K 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 46 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.2451 (OUTLIER) cc_final: 0.0753 (m-30) REVERT: A 102 HIS cc_start: -0.2719 (OUTLIER) cc_final: -0.3891 (t70) REVERT: K 102 HIS cc_start: -0.1609 (OUTLIER) cc_final: -0.3971 (t70) REVERT: E 21 PRO cc_start: 0.4870 (Cg_exo) cc_final: 0.4290 (Cg_endo) REVERT: E 27 ASP cc_start: 0.1447 (OUTLIER) cc_final: 0.0369 (p0) REVERT: I 63 MET cc_start: 0.1176 (tmm) cc_final: 0.0818 (tmm) REVERT: C 50 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6132 (m-30) REVERT: C 102 HIS cc_start: -0.3698 (OUTLIER) cc_final: -0.4445 (t70) REVERT: G 63 MET cc_start: 0.1177 (tmm) cc_final: 0.0832 (tmm) REVERT: G 102 HIS cc_start: -0.1091 (OUTLIER) cc_final: -0.3605 (t70) REVERT: B 4 GLU cc_start: 0.5313 (pm20) cc_final: 0.5064 (mm-30) REVERT: B 17 PHE cc_start: 0.3884 (t80) cc_final: 0.3184 (t80) REVERT: B 63 MET cc_start: 0.2782 (tpp) cc_final: 0.2538 (tmm) REVERT: B 81 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7904 (mm) REVERT: D 100 ILE cc_start: 0.4675 (OUTLIER) cc_final: 0.4235 (mt) REVERT: J 18 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9055 (tp) REVERT: J 63 MET cc_start: 0.0502 (ppp) cc_final: -0.0296 (ppp) REVERT: J 102 HIS cc_start: -0.0287 (OUTLIER) cc_final: -0.3719 (t70) REVERT: F 17 PHE cc_start: 0.3625 (m-80) cc_final: 0.3197 (m-80) REVERT: F 63 MET cc_start: 0.1867 (tpt) cc_final: 0.1020 (tmm) REVERT: L 102 HIS cc_start: 0.1617 (OUTLIER) cc_final: -0.0588 (t70) outliers start: 46 outliers final: 33 residues processed: 90 average time/residue: 0.1715 time to fit residues: 25.1886 Evaluate side-chains 88 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 43 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 102 HIS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 102 HIS Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 102 HIS Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 29 optimal weight: 50.0000 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 1 GLN F 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.162247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.147357 restraints weight = 36567.954| |-----------------------------------------------------------------------------| r_work (start): 0.4881 rms_B_bonded: 5.69 r_work (final): 0.4881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3261 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11064 Z= 0.256 Angle : 0.707 12.140 15024 Z= 0.367 Chirality : 0.050 0.217 1764 Planarity : 0.007 0.070 1920 Dihedral : 6.841 30.554 1406 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.77 % Allowed : 22.20 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.30 (0.23), residues: 1272 helix: -1.36 (0.41), residues: 130 sheet: -0.45 (0.27), residues: 355 loop : -2.18 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 102 PHE 0.027 0.002 PHE J 25 TYR 0.011 0.001 TYR E 53 ARG 0.004 0.001 ARG B 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1808.24 seconds wall clock time: 33 minutes 58.16 seconds (2038.16 seconds total)