Starting phenix.real_space_refine on Tue Apr 9 22:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2u_28827/04_2024/8f2u_28827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2u_28827/04_2024/8f2u_28827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2u_28827/04_2024/8f2u_28827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2u_28827/04_2024/8f2u_28827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2u_28827/04_2024/8f2u_28827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2u_28827/04_2024/8f2u_28827.pdb" } resolution = 3.53 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= 0.003 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 77 5.16 5 C 11198 2.51 5 N 3076 2.21 5 O 3333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 8": "OE1" <-> "OE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "I ASP 22": "OD1" <-> "OD2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "T ASP 136": "OD1" <-> "OD2" Residue "T GLU 208": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17684 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1466 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "B" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1601 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 6, 'TRANS': 192} Chain: "C" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1555 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "D" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1520 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "E" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1598 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 617 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1583 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "H" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1449 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "I" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1526 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "J" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1589 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "N" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 8, 'TRANS': 216} Chain breaks: 1 Chain: "T" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1364 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 156} Time building chain proxies: 9.67, per 1000 atoms: 0.55 Number of scatterers: 17684 At special positions: 0 Unit cell: (117.072, 137.668, 132.248, 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 77 16.00 O 3333 8.00 N 3076 7.00 C 11198 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: 7.32 Conformation dependent library (CDL) restraints added in 3.3 seconds 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 5 sheets defined 62.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.950A pdb=" N SER A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.673A pdb=" N ALA A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 removed outlier: 4.360A pdb=" N ALA A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.797A pdb=" N LYS A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.722A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.736A pdb=" N GLU B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.580A pdb=" N GLU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.589A pdb=" N VAL B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.575A pdb=" N ASN B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.858A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 168 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.567A pdb=" N LYS B 187 " --> pdb=" O GLU B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.695A pdb=" N ILE B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.580A pdb=" N ALA C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 38 Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.574A pdb=" N VAL C 45 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 55 through 76 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 95 through 107 removed outlier: 3.714A pdb=" N ASN C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 removed outlier: 3.619A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.612A pdb=" N LEU D 16 " --> pdb=" O PRO D 12 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 43 removed outlier: 3.770A pdb=" N SER D 35 " --> pdb=" O ARG D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 59 Processing helix chain 'D' and resid 61 through 82 removed outlier: 3.787A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 removed outlier: 3.510A pdb=" N SER D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.880A pdb=" N CYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 177 through 196 Processing helix chain 'E' and resid 30 through 40 removed outlier: 4.001A pdb=" N ARG E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 removed outlier: 3.626A pdb=" N PHE E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.617A pdb=" N VAL E 68 " --> pdb=" O CYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 99 removed outlier: 3.669A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 105 through 113 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 134 through 144 Processing helix chain 'E' and resid 193 through 221 removed outlier: 3.973A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 18 through 24 removed outlier: 4.301A pdb=" N LEU G 22 " --> pdb=" O MET G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 43 Processing helix chain 'G' and resid 47 through 62 removed outlier: 3.815A pdb=" N LEU G 51 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE G 57 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.748A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 86 Processing helix chain 'G' and resid 88 through 100 Processing helix chain 'G' and resid 102 through 127 removed outlier: 3.995A pdb=" N TYR G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Proline residue: G 118 - end of helix removed outlier: 3.750A pdb=" N ILE G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY G 126 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN G 127 " --> pdb=" O TRP G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 197 removed outlier: 3.589A pdb=" N GLU G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 13 removed outlier: 3.951A pdb=" N ARG H 11 " --> pdb=" O PRO H 8 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN H 13 " --> pdb=" O TRP H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 18 No H-bonds generated for 'chain 'H' and resid 16 through 18' Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.970A pdb=" N LEU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.507A pdb=" N ASP H 41 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS H 43 " --> pdb=" O GLN H 40 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR H 44 " --> pdb=" O ASP H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 69 removed outlier: 4.062A pdb=" N HIS H 53 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 79 removed outlier: 3.763A pdb=" N LEU H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.529A pdb=" N ILE H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 183 removed outlier: 3.769A pdb=" N VAL H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 18 removed outlier: 3.762A pdb=" N LYS I 17 " --> pdb=" O SER I 14 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA I 18 " --> pdb=" O LEU I 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 14 through 18' Processing helix chain 'I' and resid 20 through 32 removed outlier: 4.141A pdb=" N VAL I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 3.534A pdb=" N LYS I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 51 " --> pdb=" O CYS I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 75 removed outlier: 3.943A pdb=" N ALA I 57 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU I 60 " --> pdb=" O GLU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 84 removed outlier: 3.603A pdb=" N ILE I 82 " --> pdb=" O SER I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 105 removed outlier: 3.968A pdb=" N LEU I 97 " --> pdb=" O ASN I 93 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS I 105 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 114 removed outlier: 3.874A pdb=" N TRP I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 161 removed outlier: 3.788A pdb=" N CYS I 160 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 198 Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 29 through 39 removed outlier: 4.653A pdb=" N LEU J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 38 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 62 Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.707A pdb=" N LEU J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.633A pdb=" N LEU J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU J 97 " --> pdb=" O GLN J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 102 through 126 removed outlier: 6.019A pdb=" N GLN J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR J 120 " --> pdb=" O MET J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 199 Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'N' and resid 24 through 36 removed outlier: 4.176A pdb=" N GLU N 29 " --> pdb=" O VAL N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'N' and resid 48 through 64 removed outlier: 3.815A pdb=" N LYS N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR N 62 " --> pdb=" O THR N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 94 removed outlier: 4.777A pdb=" N ALA N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 98 Processing helix chain 'N' and resid 104 through 110 removed outlier: 4.323A pdb=" N GLN N 109 " --> pdb=" O PRO N 105 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 135 Proline residue: N 118 - end of helix removed outlier: 3.780A pdb=" N GLN N 121 " --> pdb=" O PHE N 117 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TRP N 122 " --> pdb=" O PRO N 118 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU N 123 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU N 132 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU N 133 " --> pdb=" O GLU N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 150 removed outlier: 4.466A pdb=" N THR N 149 " --> pdb=" O GLN N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 176 removed outlier: 3.846A pdb=" N ASP N 157 " --> pdb=" O PRO N 153 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE N 158 " --> pdb=" O GLU N 154 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS N 160 " --> pdb=" O ASP N 156 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU N 163 " --> pdb=" O ILE N 159 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS N 164 " --> pdb=" O LYS N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.867A pdb=" N HIS N 199 " --> pdb=" O GLU N 195 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU N 203 " --> pdb=" O HIS N 199 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU N 204 " --> pdb=" O ALA N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 278 Processing helix chain 'N' and resid 278 through 301 removed outlier: 5.970A pdb=" N ALA N 284 " --> pdb=" O GLY N 280 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU N 285 " --> pdb=" O LEU N 281 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER N 298 " --> pdb=" O ALA N 294 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU N 299 " --> pdb=" O GLU N 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 140 removed outlier: 4.425A pdb=" N LEU T 127 " --> pdb=" O SER T 123 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU T 140 " --> pdb=" O ASP T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 148 Processing helix chain 'T' and resid 149 through 156 Processing helix chain 'T' and resid 178 through 185 removed outlier: 3.786A pdb=" N GLU T 182 " --> pdb=" O GLY T 178 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE T 183 " --> pdb=" O GLU T 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 195 Processing helix chain 'T' and resid 198 through 219 Processing helix chain 'T' and resid 230 through 235 removed outlier: 4.173A pdb=" N LEU T 235 " --> pdb=" O THR T 232 " (cutoff:3.500A) Processing helix chain 'T' and resid 241 through 258 removed outlier: 3.937A pdb=" N ARG T 247 " --> pdb=" O ALA T 243 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU T 248 " --> pdb=" O GLN T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 274 through 280 removed outlier: 4.069A pdb=" N ALA T 278 " --> pdb=" O GLU T 274 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP T 279 " --> pdb=" O LEU T 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.713A pdb=" N ILE A 145 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 121 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY A 150 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 119 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 117 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS F 48 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 21 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA F 50 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU F 19 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET F 28 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR D 141 " --> pdb=" O MET F 28 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL F 30 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASP D 139 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER F 32 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG D 137 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 133 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 152 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 161 " --> pdb=" O GLN D 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.713A pdb=" N ILE A 145 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 121 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY A 150 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 119 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP A 124 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER I 136 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 126 " --> pdb=" O THR I 134 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL I 130 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 132 " --> pdb=" O TRP I 128 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP I 128 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU I 123 " --> pdb=" O GLN I 154 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN I 154 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP I 125 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS I 147 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 167 removed outlier: 3.870A pdb=" N ASN B 126 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN B 155 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N TYR B 124 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TRP B 129 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER H 130 " --> pdb=" O TRP B 129 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 131 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL H 124 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER B 137 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TRP H 122 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU H 117 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS H 148 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP H 119 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170 removed outlier: 3.835A pdb=" N ASP C 127 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN C 156 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE C 125 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 146 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR C 134 " --> pdb=" O GLN J 144 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN J 144 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 136 " --> pdb=" O ASN J 142 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN J 142 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR C 138 " --> pdb=" O GLN J 140 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN J 140 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY J 163 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL J 137 " --> pdb=" O GLN J 161 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLN J 161 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP J 139 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL J 159 " --> pdb=" O TRP J 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU J 141 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN J 157 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU J 143 " --> pdb=" O SER J 155 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER J 155 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 187 through 192 removed outlier: 3.702A pdb=" N VAL E 176 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 181 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 154 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG E 158 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER G 147 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP E 160 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER G 145 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA E 162 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL G 143 " --> pdb=" O ALA E 162 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN G 133 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL G 163 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET G 137 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS G 161 " --> pdb=" O MET G 137 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TRP G 139 " --> pdb=" O GLN G 159 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN G 159 " --> pdb=" O TRP G 139 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE G 141 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE G 157 " --> pdb=" O PHE G 141 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 3009 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: 5.11 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5898 1.34 - 1.46: 3571 1.46 - 1.58: 8398 1.58 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 17989 Sorted by residual: bond pdb=" N GLY E 20 " pdb=" CA GLY E 20 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.23e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N GLN N 23 " pdb=" CA GLN N 23 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N GLU H 5 " pdb=" CA GLU H 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 ... (remaining 17984 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 476 107.06 - 113.80: 10327 113.80 - 120.54: 7125 120.54 - 127.29: 6185 127.29 - 134.03: 188 Bond angle restraints: 24301 Sorted by residual: angle pdb=" C LEU E 113 " pdb=" N GLN E 114 " pdb=" CA GLN E 114 " ideal model delta sigma weight residual 121.54 133.31 -11.77 1.91e+00 2.74e-01 3.80e+01 angle pdb=" CG1 ILE J 8 " pdb=" CB ILE J 8 " pdb=" CG2 ILE J 8 " ideal model delta sigma weight residual 110.70 126.70 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" CA ILE J 99 " pdb=" CB ILE J 99 " pdb=" CG2 ILE J 99 " ideal model delta sigma weight residual 110.50 118.27 -7.77 1.70e+00 3.46e-01 2.09e+01 angle pdb=" N GLU E 115 " pdb=" CA GLU E 115 " pdb=" C GLU E 115 " ideal model delta sigma weight residual 111.75 116.79 -5.04 1.28e+00 6.10e-01 1.55e+01 angle pdb=" CG1 ILE J 99 " pdb=" CB ILE J 99 " pdb=" CG2 ILE J 99 " ideal model delta sigma weight residual 110.70 122.45 -11.75 3.00e+00 1.11e-01 1.53e+01 ... (remaining 24296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9892 17.97 - 35.93: 942 35.93 - 53.90: 170 53.90 - 71.86: 49 71.86 - 89.83: 34 Dihedral angle restraints: 11087 sinusoidal: 4552 harmonic: 6535 Sorted by residual: dihedral pdb=" C LEU E 113 " pdb=" N LEU E 113 " pdb=" CA LEU E 113 " pdb=" CB LEU E 113 " ideal model delta harmonic sigma weight residual -122.60 -132.01 9.41 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C GLU E 115 " pdb=" N GLU E 115 " pdb=" CA GLU E 115 " pdb=" CB GLU E 115 " ideal model delta harmonic sigma weight residual -122.60 -131.78 9.18 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N GLU E 115 " pdb=" C GLU E 115 " pdb=" CA GLU E 115 " pdb=" CB GLU E 115 " ideal model delta harmonic sigma weight residual 122.80 131.98 -9.18 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 11084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 2787 0.335 - 0.669: 4 0.669 - 1.004: 0 1.004 - 1.338: 0 1.338 - 1.673: 3 Chirality restraints: 2794 Sorted by residual: chirality pdb=" CB ILE J 8 " pdb=" CA ILE J 8 " pdb=" CG1 ILE J 8 " pdb=" CG2 ILE J 8 " both_signs ideal model delta sigma weight residual False 2.64 0.97 1.67 2.00e-01 2.50e+01 7.00e+01 chirality pdb=" CG LEU J 68 " pdb=" CB LEU J 68 " pdb=" CD1 LEU J 68 " pdb=" CD2 LEU J 68 " both_signs ideal model delta sigma weight residual False -2.59 -0.94 -1.65 2.00e-01 2.50e+01 6.81e+01 chirality pdb=" CB ILE J 99 " pdb=" CA ILE J 99 " pdb=" CG1 ILE J 99 " pdb=" CG2 ILE J 99 " both_signs ideal model delta sigma weight residual False 2.64 1.17 1.47 2.00e-01 2.50e+01 5.40e+01 ... (remaining 2791 not shown) Planarity restraints: 3119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 118 " -0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO E 119 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 119 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 119 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 117 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO G 118 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 118 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 118 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU T 235 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO T 236 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO T 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO T 236 " -0.028 5.00e-02 4.00e+02 ... (remaining 3116 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 126 2.57 - 3.15: 14415 3.15 - 3.73: 26301 3.73 - 4.32: 34214 4.32 - 4.90: 58647 Nonbonded interactions: 133703 Sorted by model distance: nonbonded pdb=" OD1 ASN G 23 " pdb=" OG SER G 102 " model vdw 1.983 2.440 nonbonded pdb=" OH TYR J 188 " pdb=" OG1 THR N 201 " model vdw 1.983 2.440 nonbonded pdb=" O PHE D 5 " pdb=" OG SER D 78 " model vdw 2.078 2.440 nonbonded pdb=" O GLU D 18 " pdb=" OG1 THR D 21 " model vdw 2.086 2.440 nonbonded pdb=" OG SER H 48 " pdb=" OE1 GLU H 49 " model vdw 2.092 2.440 ... (remaining 133698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.140 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 47.640 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 0.057 17989 Z= 0.165 Angle : 0.560 15.999 24301 Z= 0.310 Chirality : 0.065 1.673 2794 Planarity : 0.004 0.077 3119 Dihedral : 15.519 89.827 6815 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2210 helix: 1.80 (0.15), residues: 1183 sheet: 0.79 (0.33), residues: 269 loop : -1.18 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 59 HIS 0.005 0.001 HIS J 69 PHE 0.014 0.001 PHE G 38 TYR 0.017 0.001 TYR B 67 ARG 0.009 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.197 Fit side-chains revert: symmetry clash REVERT: C 107 ASN cc_start: 0.7638 (p0) cc_final: 0.7376 (p0) REVERT: D 1 MET cc_start: 0.4009 (ttt) cc_final: 0.3501 (ttt) REVERT: E 111 ASP cc_start: 0.4996 (m-30) cc_final: 0.4551 (m-30) REVERT: E 115 GLU cc_start: 0.5107 (mm-30) cc_final: 0.4166 (pm20) REVERT: F 48 LYS cc_start: 0.7219 (ptmt) cc_final: 0.6909 (mtpt) REVERT: H 88 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5968 (mm-30) REVERT: H 119 ASP cc_start: 0.7247 (p0) cc_final: 0.7039 (p0) REVERT: I 40 LYS cc_start: 0.6663 (tttp) cc_final: 0.5891 (ttmt) REVERT: N 112 ASP cc_start: 0.3312 (m-30) cc_final: 0.3045 (p0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3127 time to fit residues: 108.5304 Evaluate side-chains 164 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 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 21 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 106 ASN D 102 HIS D 118 GLN D 190 GLN E 95 GLN F 52 HIS I 29 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 GLN J 86 ASN N 77 ASN N 82 GLN N 147 GLN T 246 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17989 Z= 0.415 Angle : 0.736 8.310 24301 Z= 0.376 Chirality : 0.046 0.203 2794 Planarity : 0.006 0.063 3119 Dihedral : 4.690 17.353 2380 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.22 % Allowed : 9.84 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2210 helix: 0.89 (0.15), residues: 1213 sheet: 0.18 (0.30), residues: 297 loop : -1.56 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 123 HIS 0.010 0.002 HIS J 42 PHE 0.027 0.003 PHE J 30 TYR 0.019 0.002 TYR N 205 ARG 0.007 0.001 ARG J 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 2.122 Fit side-chains REVERT: B 71 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: E 115 GLU cc_start: 0.5296 (mm-30) cc_final: 0.4538 (tt0) REVERT: F 48 LYS cc_start: 0.7633 (ptmt) cc_final: 0.7139 (mtpt) REVERT: H 88 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6278 (mm-30) REVERT: H 91 MET cc_start: 0.7096 (mpp) cc_final: 0.6797 (mpp) REVERT: H 119 ASP cc_start: 0.7964 (p0) cc_final: 0.7745 (p0) REVERT: J 75 ILE cc_start: 0.7843 (mm) cc_final: 0.7457 (mt) REVERT: N 66 PHE cc_start: 0.4147 (OUTLIER) cc_final: 0.3177 (t80) REVERT: N 287 LYS cc_start: 0.3977 (ttmt) cc_final: 0.3532 (tppt) outliers start: 24 outliers final: 13 residues processed: 183 average time/residue: 0.3129 time to fit residues: 87.6542 Evaluate side-chains 164 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 168 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN D 190 GLN F 52 HIS I 29 GLN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17989 Z= 0.154 Angle : 0.523 8.802 24301 Z= 0.267 Chirality : 0.037 0.161 2794 Planarity : 0.004 0.048 3119 Dihedral : 4.123 17.930 2380 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.22 % Allowed : 11.98 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2210 helix: 1.34 (0.15), residues: 1229 sheet: 0.49 (0.30), residues: 289 loop : -1.37 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 123 HIS 0.011 0.001 HIS J 42 PHE 0.023 0.001 PHE D 5 TYR 0.011 0.001 TYR B 67 ARG 0.004 0.000 ARG J 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 PHE cc_start: 0.6232 (t80) cc_final: 0.5953 (t80) REVERT: B 71 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: E 115 GLU cc_start: 0.5254 (mm-30) cc_final: 0.3980 (pm20) REVERT: F 48 LYS cc_start: 0.7500 (ptmt) cc_final: 0.7029 (mtpt) REVERT: G 1 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.2886 (ttm) REVERT: H 91 MET cc_start: 0.7272 (mpp) cc_final: 0.6907 (mpp) REVERT: I 83 LEU cc_start: 0.2889 (OUTLIER) cc_final: 0.2582 (tt) REVERT: J 75 ILE cc_start: 0.7862 (mm) cc_final: 0.7544 (mt) REVERT: N 66 PHE cc_start: 0.4060 (OUTLIER) cc_final: 0.3139 (t80) REVERT: N 160 LYS cc_start: 0.7145 (mtmm) cc_final: 0.6193 (tptp) REVERT: N 287 LYS cc_start: 0.3829 (ttmt) cc_final: 0.3453 (tppt) outliers start: 24 outliers final: 14 residues processed: 185 average time/residue: 0.3137 time to fit residues: 87.9375 Evaluate side-chains 170 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 4.9990 chunk 147 optimal weight: 0.0030 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN F 52 HIS G 80 ASN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17989 Z= 0.179 Angle : 0.518 9.002 24301 Z= 0.263 Chirality : 0.037 0.145 2794 Planarity : 0.004 0.047 3119 Dihedral : 4.005 17.303 2380 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.48 % Allowed : 13.51 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2210 helix: 1.48 (0.15), residues: 1223 sheet: 0.57 (0.31), residues: 287 loop : -1.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 51 HIS 0.009 0.001 HIS J 42 PHE 0.020 0.001 PHE D 5 TYR 0.010 0.001 TYR D 48 ARG 0.004 0.000 ARG J 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 2.076 Fit side-chains revert: symmetry clash REVERT: B 71 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6661 (pm20) REVERT: B 186 MET cc_start: 0.7262 (tpp) cc_final: 0.7053 (tpp) REVERT: E 115 GLU cc_start: 0.5495 (mm-30) cc_final: 0.4166 (pm20) REVERT: F 48 LYS cc_start: 0.7499 (ptmt) cc_final: 0.7130 (mtpt) REVERT: G 1 MET cc_start: 0.3484 (OUTLIER) cc_final: 0.2773 (ttm) REVERT: G 123 TRP cc_start: 0.6695 (t60) cc_final: 0.6415 (t60) REVERT: H 91 MET cc_start: 0.7349 (mpp) cc_final: 0.6971 (mpp) REVERT: I 83 LEU cc_start: 0.2850 (OUTLIER) cc_final: 0.2527 (tt) REVERT: J 75 ILE cc_start: 0.8062 (mm) cc_final: 0.7678 (mt) REVERT: N 64 CYS cc_start: 0.2471 (OUTLIER) cc_final: 0.2258 (t) REVERT: N 66 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3187 (t80) REVERT: T 250 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7102 (tttm) outliers start: 29 outliers final: 16 residues processed: 183 average time/residue: 0.2993 time to fit residues: 84.1798 Evaluate side-chains 172 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 64 CYS Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain T residue 250 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 0.0970 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 118 GLN F 52 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17989 Z= 0.204 Angle : 0.529 9.167 24301 Z= 0.268 Chirality : 0.038 0.143 2794 Planarity : 0.004 0.049 3119 Dihedral : 4.024 16.459 2380 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.83 % Allowed : 14.53 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2210 helix: 1.42 (0.15), residues: 1235 sheet: 0.57 (0.31), residues: 288 loop : -1.30 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 59 HIS 0.004 0.001 HIS J 42 PHE 0.018 0.001 PHE D 5 TYR 0.013 0.001 TYR N 176 ARG 0.003 0.000 ARG J 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 2.442 Fit side-chains revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6661 (pm20) REVERT: E 115 GLU cc_start: 0.5444 (mm-30) cc_final: 0.4154 (pm20) REVERT: F 48 LYS cc_start: 0.7545 (ptmt) cc_final: 0.7051 (mtpt) REVERT: G 1 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.2781 (ttm) REVERT: G 123 TRP cc_start: 0.6655 (t60) cc_final: 0.6357 (t60) REVERT: H 91 MET cc_start: 0.7386 (mpp) cc_final: 0.7050 (mpp) REVERT: I 83 LEU cc_start: 0.2856 (OUTLIER) cc_final: 0.2547 (tt) REVERT: J 75 ILE cc_start: 0.8077 (mm) cc_final: 0.7701 (mt) REVERT: N 66 PHE cc_start: 0.4122 (OUTLIER) cc_final: 0.3270 (t80) outliers start: 36 outliers final: 21 residues processed: 184 average time/residue: 0.3206 time to fit residues: 92.0612 Evaluate side-chains 176 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.5980 chunk 188 optimal weight: 9.9990 chunk 41 optimal weight: 0.0570 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 109 optimal weight: 0.0060 overall best weight: 0.7316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17989 Z= 0.129 Angle : 0.473 9.009 24301 Z= 0.239 Chirality : 0.036 0.136 2794 Planarity : 0.004 0.048 3119 Dihedral : 3.724 17.469 2380 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.33 % Allowed : 15.34 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2210 helix: 1.77 (0.15), residues: 1232 sheet: 0.83 (0.31), residues: 288 loop : -1.16 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 59 HIS 0.004 0.000 HIS J 42 PHE 0.022 0.001 PHE D 5 TYR 0.009 0.001 TYR D 48 ARG 0.004 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.5118 (mm-30) cc_final: 0.4892 (mm-30) REVERT: B 71 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: E 115 GLU cc_start: 0.5593 (mm-30) cc_final: 0.4242 (pm20) REVERT: F 48 LYS cc_start: 0.7449 (ptmt) cc_final: 0.7067 (mtpt) REVERT: G 1 MET cc_start: 0.3337 (OUTLIER) cc_final: 0.2673 (ttm) REVERT: H 91 MET cc_start: 0.7368 (mpp) cc_final: 0.7033 (mpp) REVERT: H 119 ASP cc_start: 0.7362 (p0) cc_final: 0.7048 (p0) REVERT: I 83 LEU cc_start: 0.2780 (OUTLIER) cc_final: 0.2477 (tt) REVERT: J 75 ILE cc_start: 0.7979 (mm) cc_final: 0.7604 (mt) REVERT: N 66 PHE cc_start: 0.4001 (OUTLIER) cc_final: 0.3109 (t80) REVERT: N 160 LYS cc_start: 0.7185 (mtmm) cc_final: 0.6272 (tptp) outliers start: 26 outliers final: 15 residues processed: 194 average time/residue: 0.2974 time to fit residues: 88.6563 Evaluate side-chains 181 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 171 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17989 Z= 0.229 Angle : 0.548 9.199 24301 Z= 0.275 Chirality : 0.038 0.143 2794 Planarity : 0.004 0.049 3119 Dihedral : 3.955 16.273 2380 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.58 % Allowed : 16.11 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2210 helix: 1.50 (0.15), residues: 1243 sheet: 0.72 (0.31), residues: 291 loop : -1.36 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 59 HIS 0.004 0.001 HIS I 65 PHE 0.016 0.002 PHE D 5 TYR 0.010 0.001 TYR D 48 ARG 0.004 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: A 165 GLU cc_start: 0.5436 (mm-30) cc_final: 0.5211 (mm-30) REVERT: D 51 ILE cc_start: 0.7956 (pt) cc_final: 0.7671 (pt) REVERT: E 115 GLU cc_start: 0.5613 (mm-30) cc_final: 0.4252 (pm20) REVERT: F 48 LYS cc_start: 0.7549 (ptmt) cc_final: 0.7027 (mtpt) REVERT: G 1 MET cc_start: 0.3298 (OUTLIER) cc_final: 0.2671 (ttm) REVERT: H 91 MET cc_start: 0.7408 (mpp) cc_final: 0.7088 (mpp) REVERT: H 119 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7125 (p0) REVERT: I 83 LEU cc_start: 0.3103 (OUTLIER) cc_final: 0.2783 (tt) REVERT: J 75 ILE cc_start: 0.8094 (mm) cc_final: 0.7716 (mt) REVERT: N 66 PHE cc_start: 0.4058 (OUTLIER) cc_final: 0.3216 (t80) outliers start: 31 outliers final: 22 residues processed: 189 average time/residue: 0.2823 time to fit residues: 84.2352 Evaluate side-chains 187 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 286 ILE Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 HIS ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS G 80 ASN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17989 Z= 0.259 Angle : 0.575 9.582 24301 Z= 0.291 Chirality : 0.039 0.148 2794 Planarity : 0.004 0.050 3119 Dihedral : 4.164 16.402 2380 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.78 % Allowed : 16.16 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2210 helix: 1.34 (0.15), residues: 1232 sheet: 0.51 (0.31), residues: 298 loop : -1.45 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 59 HIS 0.004 0.001 HIS A 101 PHE 0.022 0.002 PHE E 54 TYR 0.011 0.002 TYR N 205 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 2.059 Fit side-chains revert: symmetry clash REVERT: B 71 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: E 39 LEU cc_start: 0.7647 (tp) cc_final: 0.7430 (tp) REVERT: E 115 GLU cc_start: 0.5611 (mm-30) cc_final: 0.4833 (tt0) REVERT: F 48 LYS cc_start: 0.7521 (ptmt) cc_final: 0.7033 (mtpt) REVERT: G 1 MET cc_start: 0.3661 (OUTLIER) cc_final: 0.3172 (ttm) REVERT: H 91 MET cc_start: 0.7471 (mpp) cc_final: 0.7147 (mpp) REVERT: H 119 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7274 (p0) REVERT: I 83 LEU cc_start: 0.3236 (OUTLIER) cc_final: 0.2945 (tt) REVERT: J 75 ILE cc_start: 0.8173 (mm) cc_final: 0.7759 (mt) REVERT: N 66 PHE cc_start: 0.4038 (OUTLIER) cc_final: 0.3226 (t80) outliers start: 35 outliers final: 27 residues processed: 187 average time/residue: 0.2994 time to fit residues: 86.4529 Evaluate side-chains 187 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 65 HIS Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 286 ILE Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 0.0670 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS G 80 ASN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17989 Z= 0.148 Angle : 0.503 9.383 24301 Z= 0.253 Chirality : 0.037 0.187 2794 Planarity : 0.004 0.050 3119 Dihedral : 3.848 17.720 2380 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.48 % Allowed : 16.62 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2210 helix: 1.62 (0.15), residues: 1242 sheet: 0.72 (0.31), residues: 291 loop : -1.32 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 59 HIS 0.003 0.001 HIS J 147 PHE 0.018 0.001 PHE N 146 TYR 0.011 0.001 TYR D 48 ARG 0.002 0.000 ARG J 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 2.114 Fit side-chains REVERT: B 71 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: D 51 ILE cc_start: 0.7951 (pt) cc_final: 0.7695 (pt) REVERT: E 115 GLU cc_start: 0.5517 (mm-30) cc_final: 0.4784 (tt0) REVERT: F 48 LYS cc_start: 0.7492 (ptmt) cc_final: 0.6985 (mtpt) REVERT: G 1 MET cc_start: 0.3760 (OUTLIER) cc_final: 0.3161 (ttm) REVERT: H 91 MET cc_start: 0.7366 (mpp) cc_final: 0.7065 (mpp) REVERT: H 119 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6990 (p0) REVERT: I 83 LEU cc_start: 0.3250 (OUTLIER) cc_final: 0.2943 (tt) REVERT: J 75 ILE cc_start: 0.8064 (mm) cc_final: 0.7707 (mt) REVERT: N 66 PHE cc_start: 0.4191 (OUTLIER) cc_final: 0.3455 (t80) outliers start: 29 outliers final: 19 residues processed: 189 average time/residue: 0.2869 time to fit residues: 84.8385 Evaluate side-chains 184 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17989 Z= 0.186 Angle : 0.527 9.484 24301 Z= 0.264 Chirality : 0.037 0.142 2794 Planarity : 0.004 0.050 3119 Dihedral : 3.887 17.045 2380 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.33 % Allowed : 16.67 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2210 helix: 1.59 (0.15), residues: 1235 sheet: 0.70 (0.31), residues: 291 loop : -1.34 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 59 HIS 0.003 0.001 HIS J 147 PHE 0.019 0.001 PHE N 146 TYR 0.012 0.001 TYR D 48 ARG 0.002 0.000 ARG J 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4420 Ramachandran restraints generated. 2210 Oldfield, 0 Emsley, 2210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 2.143 Fit side-chains revert: symmetry clash REVERT: B 71 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: D 51 ILE cc_start: 0.7923 (pt) cc_final: 0.7677 (pt) REVERT: E 110 ARG cc_start: 0.7125 (mtm180) cc_final: 0.6894 (mtm110) REVERT: E 115 GLU cc_start: 0.5543 (mm-30) cc_final: 0.4831 (tt0) REVERT: F 48 LYS cc_start: 0.7481 (ptmt) cc_final: 0.7019 (mtpt) REVERT: G 1 MET cc_start: 0.3635 (OUTLIER) cc_final: 0.3088 (ttm) REVERT: H 91 MET cc_start: 0.7370 (mpp) cc_final: 0.7082 (mpp) REVERT: H 119 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7034 (p0) REVERT: I 83 LEU cc_start: 0.3259 (OUTLIER) cc_final: 0.2955 (tt) REVERT: J 75 ILE cc_start: 0.8084 (mm) cc_final: 0.7716 (mt) REVERT: N 66 PHE cc_start: 0.4194 (OUTLIER) cc_final: 0.3471 (t80) REVERT: N 292 GLU cc_start: 0.3910 (tp30) cc_final: 0.2676 (pt0) outliers start: 26 outliers final: 21 residues processed: 185 average time/residue: 0.2877 time to fit residues: 82.8803 Evaluate side-chains 188 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 65 HIS Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 139 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 66 PHE Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 289 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.158516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.133540 restraints weight = 32423.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132990 restraints weight = 57585.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133877 restraints weight = 49260.680| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17989 Z= 0.248 Angle : 0.574 9.699 24301 Z= 0.288 Chirality : 0.039 0.146 2794 Planarity : 0.004 0.050 3119 Dihedral : 4.118 16.562 2380 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.48 % Allowed : 16.62 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2210 helix: 1.41 (0.15), residues: 1232 sheet: 0.52 (0.31), residues: 297 loop : -1.43 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 59 HIS 0.004 0.001 HIS J 147 PHE 0.020 0.002 PHE N 146 TYR 0.013 0.002 TYR D 48 ARG 0.003 0.000 ARG D 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.72 seconds wall clock time: 54 minutes 49.87 seconds (3289.87 seconds total)