Starting phenix.real_space_refine on Sun Aug 4 15:05:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3p_44148/08_2024/9b3p_44148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3p_44148/08_2024/9b3p_44148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3p_44148/08_2024/9b3p_44148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3p_44148/08_2024/9b3p_44148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3p_44148/08_2024/9b3p_44148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3p_44148/08_2024/9b3p_44148.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 256 5.49 5 S 10 5.16 5 C 6151 2.51 5 N 2078 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 75": "OD1" <-> "OD2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11067 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 797 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 740 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 776 Classifications: {'peptide': 102} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2639 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "J" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2609 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Time building chain proxies: 6.40, per 1000 atoms: 0.58 Number of scatterers: 11067 At special positions: 0 Unit cell: (103.68, 115.56, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 256 15.00 O 2572 8.00 N 2078 7.00 C 6151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 69.4% alpha, 1.1% beta 12 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.704A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.507A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.731A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 4.164A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.681A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.772A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.967A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.533A pdb=" N ARG C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.709A pdb=" N ILE C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 39 " --> pdb=" O HIS C 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 removed outlier: 3.887A pdb=" N ALA C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 56 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.585A pdb=" N LEU C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.771A pdb=" N SER C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 100' Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.651A pdb=" N VAL D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.564A pdb=" N SER D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.886A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.801A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.573A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 3.637A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.582A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.806A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.255A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 29' Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.708A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.666A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.817A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 removed outlier: 3.648A pdb=" N ARG G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 23 " --> pdb=" O ARG G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 removed outlier: 3.672A pdb=" N ILE G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.858A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 57 " --> pdb=" O TYR G 53 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.533A pdb=" N LEU G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.550A pdb=" N LEU G 117 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G 118 " --> pdb=" O LYS G 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 118' Processing helix chain 'H' and resid 40 through 49 removed outlier: 3.659A pdb=" N VAL H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.972A pdb=" N SER H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.999A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.998A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 46 removed outlier: 7.077A pdb=" N ARG C 45 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.808A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 removed outlier: 6.322A pdb=" N ARG G 45 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 240 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2443 1.34 - 1.45: 3593 1.45 - 1.57: 5222 1.57 - 1.69: 510 1.69 - 1.81: 18 Bond restraints: 11786 Sorted by residual: bond pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.25e-01 bond pdb=" C3' DT I -50 " pdb=" O3' DT I -50 " ideal model delta sigma weight residual 1.422 1.447 -0.025 3.00e-02 1.11e+03 6.98e-01 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.446 -0.024 3.00e-02 1.11e+03 6.62e-01 bond pdb=" C THR H 90 " pdb=" O THR H 90 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.17e-02 7.31e+03 4.90e-01 ... (remaining 11781 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.12: 1765 107.12 - 113.45: 6291 113.45 - 119.78: 3480 119.78 - 126.11: 4683 126.11 - 132.45: 793 Bond angle restraints: 17012 Sorted by residual: angle pdb=" C THR H 90 " pdb=" CA THR H 90 " pdb=" CB THR H 90 " ideal model delta sigma weight residual 114.40 110.29 4.11 1.25e+00 6.40e-01 1.08e+01 angle pdb=" C LEU C 76 " pdb=" N LYS C 77 " pdb=" CA LYS C 77 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 angle pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " pdb=" P DA I -31 " ideal model delta sigma weight residual 120.20 122.92 -2.72 1.50e+00 4.44e-01 3.29e+00 angle pdb=" C7 DT I 15 " pdb=" C5 DT I 15 " pdb=" C6 DT I 15 " ideal model delta sigma weight residual 124.00 121.74 2.26 1.50e+00 4.44e-01 2.27e+00 angle pdb=" C7 DT J 1 " pdb=" C5 DT J 1 " pdb=" C6 DT J 1 " ideal model delta sigma weight residual 124.00 121.74 2.26 1.50e+00 4.44e-01 2.27e+00 ... (remaining 17007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 5475 34.64 - 69.28: 926 69.28 - 103.92: 7 103.92 - 138.55: 1 138.55 - 173.19: 2 Dihedral angle restraints: 6411 sinusoidal: 4281 harmonic: 2130 Sorted by residual: dihedral pdb=" C4' DT I -32 " pdb=" C3' DT I -32 " pdb=" O3' DT I -32 " pdb=" P DA I -31 " ideal model delta sinusoidal sigma weight residual -140.00 33.19 -173.19 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 80.29 139.71 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" C4' DT I -50 " pdb=" C3' DT I -50 " pdb=" O3' DT I -50 " pdb=" P DG I -49 " ideal model delta sinusoidal sigma weight residual 220.00 84.81 135.19 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 6408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1510 0.025 - 0.051: 300 0.051 - 0.076: 83 0.076 - 0.101: 30 0.101 - 0.127: 18 Chirality restraints: 1941 Sorted by residual: chirality pdb=" CA ILE H 54 " pdb=" N ILE H 54 " pdb=" C ILE H 54 " pdb=" CB ILE H 54 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE C 110 " pdb=" N ILE C 110 " pdb=" C ILE C 110 " pdb=" CB ILE C 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE G 110 " pdb=" N ILE G 110 " pdb=" C ILE G 110 " pdb=" CB ILE G 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 1938 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 82 " -0.013 5.00e-02 4.00e+02 1.93e-02 5.99e-01 pdb=" N PRO G 83 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 82 " -0.012 5.00e-02 4.00e+02 1.82e-02 5.29e-01 pdb=" N PRO C 83 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.012 5.00e-02 4.00e+02 1.75e-02 4.88e-01 pdb=" N PRO A 121 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.010 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2628 2.81 - 3.34: 8621 3.34 - 3.86: 18528 3.86 - 4.38: 22781 4.38 - 4.90: 33678 Nonbonded interactions: 86236 Sorted by model distance: nonbonded pdb=" OG1 THR C 41 " pdb=" N SER C 42 " model vdw 2.292 3.120 nonbonded pdb=" OG1 THR G 41 " pdb=" N SER G 42 " model vdw 2.311 3.120 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG I 48 " model vdw 2.337 3.040 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.376 3.120 nonbonded pdb=" O HIS G 43 " pdb=" OG SER H 87 " model vdw 2.377 3.040 ... (remaining 86231 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 'E' and resid 38 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 17 through 113) selection = (chain 'G' and resid 17 through 113) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.990 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.370 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11786 Z= 0.102 Angle : 0.374 4.949 17012 Z= 0.250 Chirality : 0.027 0.127 1941 Planarity : 0.002 0.019 1262 Dihedral : 24.092 173.192 5039 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.57 % Favored : 94.88 % Rotamer: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -5.86 (0.18), residues: 722 helix: -4.69 (0.06), residues: 424 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 82 PHE 0.001 0.000 PHE F 100 TYR 0.001 0.000 TYR F 72 ARG 0.001 0.000 ARG G 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.826 Fit side-chains REVERT: G 64 GLU cc_start: 0.7722 (tp30) cc_final: 0.7507 (mm-30) REVERT: G 87 GLN cc_start: 0.8141 (tp40) cc_final: 0.7869 (tp40) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 1.5594 time to fit residues: 254.1817 Evaluate side-chains 93 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 63 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 26 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 11786 Z= 0.226 Angle : 0.544 11.606 17012 Z= 0.310 Chirality : 0.033 0.129 1941 Planarity : 0.004 0.033 1262 Dihedral : 27.622 170.130 3621 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.94 % Favored : 97.78 % Rotamer: Outliers : 2.63 % Allowed : 14.80 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.96 (0.24), residues: 722 helix: -1.66 (0.19), residues: 474 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.011 0.001 PHE F 61 TYR 0.015 0.002 TYR C 53 ARG 0.005 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.884 Fit side-chains REVERT: D 95 GLN cc_start: 0.8435 (tt0) cc_final: 0.8213 (tt0) REVERT: E 48 LEU cc_start: 0.8608 (mt) cc_final: 0.8220 (mp) REVERT: F 74 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7403 (mt-10) REVERT: F 95 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7233 (mtt180) REVERT: H 93 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7106 (mp0) outliers start: 16 outliers final: 5 residues processed: 133 average time/residue: 1.7821 time to fit residues: 249.7445 Evaluate side-chains 110 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 25 ASN G 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11786 Z= 0.427 Angle : 0.698 8.011 17012 Z= 0.390 Chirality : 0.043 0.241 1941 Planarity : 0.005 0.040 1262 Dihedral : 29.305 179.077 3618 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.46 % Favored : 96.26 % Rotamer: Outliers : 3.45 % Allowed : 15.79 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.28), residues: 722 helix: -0.76 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.89 (0.33), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.014 0.003 PHE E 78 TYR 0.020 0.002 TYR E 54 ARG 0.017 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.824 Fit side-chains REVERT: D 57 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7947 (mmtt) REVERT: E 48 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8628 (mp) REVERT: E 50 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7933 (mt-10) REVERT: E 54 TYR cc_start: 0.8728 (m-80) cc_final: 0.8526 (m-80) REVERT: E 76 GLN cc_start: 0.7962 (tt0) cc_final: 0.7692 (tt0) REVERT: E 83 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7621 (mtm180) REVERT: E 133 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7764 (mt-10) REVERT: F 74 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7790 (mt-10) REVERT: G 37 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8321 (mtpt) REVERT: G 60 TYR cc_start: 0.8857 (t80) cc_final: 0.8455 (t80) REVERT: H 35 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7273 (pt0) REVERT: H 56 SER cc_start: 0.8503 (t) cc_final: 0.8233 (m) outliers start: 21 outliers final: 7 residues processed: 162 average time/residue: 1.7159 time to fit residues: 292.9719 Evaluate side-chains 125 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11786 Z= 0.202 Angle : 0.504 5.244 17012 Z= 0.295 Chirality : 0.032 0.146 1941 Planarity : 0.004 0.042 1262 Dihedral : 28.970 176.611 3618 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.96 % Allowed : 18.91 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.30), residues: 722 helix: 0.41 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 82 PHE 0.012 0.001 PHE F 61 TYR 0.009 0.001 TYR H 121 ARG 0.005 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 0.873 Fit side-chains REVERT: A 65 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8715 (mt) REVERT: B 79 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8084 (mttm) REVERT: C 21 GLN cc_start: 0.7538 (tt0) cc_final: 0.6916 (tt0) REVERT: E 50 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7773 (mt-10) REVERT: E 76 GLN cc_start: 0.7973 (tt0) cc_final: 0.7660 (tt0) REVERT: E 116 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8007 (ttp-170) REVERT: F 74 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7602 (mt-10) REVERT: H 93 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7324 (mp0) outliers start: 18 outliers final: 9 residues processed: 146 average time/residue: 1.5924 time to fit residues: 246.1566 Evaluate side-chains 135 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0170 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11786 Z= 0.164 Angle : 0.484 6.278 17012 Z= 0.286 Chirality : 0.032 0.158 1941 Planarity : 0.003 0.034 1262 Dihedral : 28.979 177.059 3618 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.29 % Allowed : 18.91 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.31), residues: 722 helix: 1.18 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 82 PHE 0.008 0.001 PHE F 61 TYR 0.009 0.001 TYR H 121 ARG 0.007 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.889 Fit side-chains REVERT: A 65 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 79 LYS cc_start: 0.7396 (tttm) cc_final: 0.7137 (tttm) REVERT: B 63 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: B 79 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8078 (mttm) REVERT: C 21 GLN cc_start: 0.7531 (tt0) cc_final: 0.6884 (tt0) REVERT: E 76 GLN cc_start: 0.7933 (tt0) cc_final: 0.7656 (tt0) REVERT: F 74 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7660 (mt-10) REVERT: G 60 TYR cc_start: 0.8782 (t80) cc_final: 0.8560 (t80) REVERT: H 93 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7311 (mp0) outliers start: 20 outliers final: 8 residues processed: 141 average time/residue: 1.7144 time to fit residues: 254.9472 Evaluate side-chains 135 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS D 82 HIS E 68 GLN H 47 GLN H 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.8022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 11786 Z= 0.436 Angle : 0.651 8.871 17012 Z= 0.369 Chirality : 0.042 0.161 1941 Planarity : 0.005 0.039 1262 Dihedral : 29.799 167.664 3618 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.11 % Allowed : 18.59 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.31), residues: 722 helix: 0.95 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.014 0.003 PHE E 78 TYR 0.017 0.002 TYR A 54 ARG 0.006 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.871 Fit side-chains REVERT: A 59 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: B 63 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: B 79 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8029 (mttm) REVERT: E 76 GLN cc_start: 0.8087 (tt0) cc_final: 0.7776 (tt0) REVERT: F 74 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7851 (mt-10) REVERT: G 37 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8223 (mtpt) REVERT: H 93 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7428 (mp0) outliers start: 25 outliers final: 12 residues processed: 140 average time/residue: 1.6132 time to fit residues: 238.8166 Evaluate side-chains 132 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS D 82 HIS E 68 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.7979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11786 Z= 0.194 Angle : 0.513 9.054 17012 Z= 0.303 Chirality : 0.033 0.145 1941 Planarity : 0.004 0.036 1262 Dihedral : 29.356 169.559 3618 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.80 % Allowed : 19.90 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.32), residues: 722 helix: 1.46 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.44 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 82 PHE 0.007 0.001 PHE E 84 TYR 0.015 0.001 TYR C 60 ARG 0.007 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.902 Fit side-chains REVERT: A 65 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 63 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: C 21 GLN cc_start: 0.7453 (tt0) cc_final: 0.6822 (tt0) REVERT: E 76 GLN cc_start: 0.8015 (tt0) cc_final: 0.7700 (tt0) REVERT: F 74 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7843 (mt-10) REVERT: G 37 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8151 (mtpt) REVERT: H 93 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7373 (mp0) outliers start: 17 outliers final: 10 residues processed: 135 average time/residue: 1.7214 time to fit residues: 246.3805 Evaluate side-chains 132 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS D 82 HIS E 68 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.8130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11786 Z= 0.251 Angle : 0.542 9.336 17012 Z= 0.316 Chirality : 0.034 0.152 1941 Planarity : 0.004 0.042 1262 Dihedral : 29.503 165.391 3618 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.12 % Allowed : 19.57 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.32), residues: 722 helix: 1.53 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.36 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 82 PHE 0.009 0.002 PHE E 84 TYR 0.013 0.001 TYR C 60 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.777 Fit side-chains REVERT: E 76 GLN cc_start: 0.7979 (tt0) cc_final: 0.7678 (tt0) REVERT: F 74 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7843 (mt-10) REVERT: G 37 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8178 (mtpt) REVERT: G 95 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: H 93 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7377 (mp0) outliers start: 19 outliers final: 12 residues processed: 129 average time/residue: 1.6032 time to fit residues: 218.9596 Evaluate side-chains 133 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.8281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11786 Z= 0.277 Angle : 0.556 9.799 17012 Z= 0.322 Chirality : 0.035 0.135 1941 Planarity : 0.004 0.044 1262 Dihedral : 29.558 165.403 3618 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.12 % Allowed : 19.90 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.32), residues: 722 helix: 1.54 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 82 PHE 0.008 0.002 PHE E 84 TYR 0.016 0.001 TYR G 60 ARG 0.005 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.749 Fit side-chains REVERT: E 76 GLN cc_start: 0.7984 (tt0) cc_final: 0.7703 (tt0) REVERT: F 74 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7808 (mt-10) REVERT: G 37 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8158 (mtpt) REVERT: G 95 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: H 93 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7380 (mp0) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 1.5856 time to fit residues: 213.7440 Evaluate side-chains 134 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN F 75 HIS H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11786 Z= 0.204 Angle : 0.535 10.236 17012 Z= 0.313 Chirality : 0.033 0.146 1941 Planarity : 0.004 0.040 1262 Dihedral : 29.523 165.233 3618 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.30 % Allowed : 21.55 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.32), residues: 722 helix: 1.71 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 82 PHE 0.007 0.001 PHE E 84 TYR 0.013 0.001 TYR C 60 ARG 0.009 0.000 ARG D 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.844 Fit side-chains REVERT: E 76 GLN cc_start: 0.7966 (tt0) cc_final: 0.7696 (tt0) REVERT: F 74 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7786 (mt-10) REVERT: G 37 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8147 (mtpt) REVERT: G 95 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: H 93 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7362 (mp0) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 1.6483 time to fit residues: 225.1900 Evaluate side-chains 132 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 68 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107974 restraints weight = 13092.311| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 0.80 r_work: 0.3007 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.8277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11786 Z= 0.195 Angle : 0.531 11.734 17012 Z= 0.310 Chirality : 0.033 0.138 1941 Planarity : 0.004 0.037 1262 Dihedral : 29.487 164.991 3618 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.63 % Allowed : 21.38 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.32), residues: 722 helix: 1.79 (0.24), residues: 523 sheet: None (None), residues: 0 loop : -1.22 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.006 0.001 PHE E 84 TYR 0.013 0.001 TYR C 60 ARG 0.005 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4215.90 seconds wall clock time: 73 minutes 41.57 seconds (4421.57 seconds total)