Starting phenix.real_space_refine on Sun Feb 25 07:49:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/02_2024/7oe0_12856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/02_2024/7oe0_12856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/02_2024/7oe0_12856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/02_2024/7oe0_12856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/02_2024/7oe0_12856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/02_2024/7oe0_12856.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1509 5.49 5 S 61 5.16 5 C 25327 2.51 5 N 9283 2.21 5 O 14116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O GLU 25": "OE1" <-> "OE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "T GLU 14": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50296 Number of models: 1 Model: "" Number of chains: 29 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 702 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 407 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "A" Number of atoms: 32408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1510, 32408 Classifications: {'RNA': 1510} Modifications used: {'5*END': 1, 'rna2p_pur': 115, 'rna2p_pyr': 81, 'rna3p_pur': 749, 'rna3p_pyr': 565} Link IDs: {'rna2p': 196, 'rna3p': 1313} Chain breaks: 2 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 642 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 484 Classifications: {'water': 484} Link IDs: {None: 483} Time building chain proxies: 26.61, per 1000 atoms: 0.53 Number of scatterers: 50296 At special positions: 0 Unit cell: (139.32, 196.08, 242.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 1509 15.00 O 14116 8.00 N 9283 7.00 C 25327 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: 28.67 Conformation dependent library (CDL) restraints added in 3.6 seconds 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 24 sheets defined 41.2% alpha, 14.7% beta 506 base pairs and 838 stacking pairs defined. Time for finding SS restraints: 26.34 Creating SS restraints... Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 62 removed outlier: 4.254A pdb=" N PHE B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 102 through 127 removed outlier: 3.646A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.719A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.829A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 3.799A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.605A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.776A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.964A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 68 Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 131 through 145 Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'F' and resid 13 through 16 removed outlier: 3.924A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 13 through 16' Processing helix chain 'F' and resid 17 through 32 Processing helix chain 'F' and resid 50 through 54 Processing helix chain 'F' and resid 71 through 81 Processing helix chain 'H' and resid 4 through 19 Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.938A pdb=" N LEU H 91 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 118 Processing helix chain 'K' and resid 58 through 72 Processing helix chain 'K' and resid 91 through 101 Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'L' and resid 20 through 24 Processing helix chain 'L' and resid 112 through 116 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 23 through 45 removed outlier: 3.981A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS O 45 " --> pdb=" O HIS O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 73 removed outlier: 4.116A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 84 removed outlier: 3.950A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 4.008A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'R' and resid 25 through 32 removed outlier: 3.615A pdb=" N LYS R 29 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASN R 30 " --> pdb=" O THR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.766A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 65 Processing helix chain 'T' and resid 3 through 39 removed outlier: 3.521A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 63 Proline residue: T 55 - end of helix Processing helix chain 'T' and resid 67 through 86 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 24 through 44 removed outlier: 3.930A pdb=" N ALA C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.835A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.517A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.523A pdb=" N ALA C 132 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 29 removed outlier: 3.810A pdb=" N ILE G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 47 removed outlier: 3.715A pdb=" N SER G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 45 " --> pdb=" O ILE G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 removed outlier: 3.717A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 104 " --> pdb=" O MET G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 127 removed outlier: 4.057A pdb=" N ALA G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 38 Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.512A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 removed outlier: 3.697A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 3.515A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'M' and resid 16 through 21 removed outlier: 3.815A pdb=" N ILE M 21 " --> pdb=" O LEU M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 35 Processing helix chain 'M' and resid 43 through 47 removed outlier: 4.034A pdb=" N LEU M 47 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 60 removed outlier: 3.802A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 79 removed outlier: 4.634A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET M 74 " --> pdb=" O ARG M 70 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU M 79 " --> pdb=" O SER M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 90 Processing helix chain 'N' and resid 2 through 23 removed outlier: 3.752A pdb=" N ARG N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU N 9 " --> pdb=" O MET N 5 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE N 20 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 32 removed outlier: 5.065A pdb=" N ILE N 29 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE N 30 " --> pdb=" O LEU N 26 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 50 removed outlier: 3.745A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 79 through 89 removed outlier: 3.766A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 16 removed outlier: 4.179A pdb=" N LEU S 15 " --> pdb=" O ASP S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 21 Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.598A pdb=" N ILE S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 74 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.967A pdb=" N ILE B 39 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA B 33 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 69 removed outlier: 5.360A pdb=" N LEU B 67 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL B 182 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 122 through 124 Processing sheet with id=AA4, first strand: chain 'D' and resid 170 through 173 Processing sheet with id=AA5, first strand: chain 'E' and resid 11 through 18 removed outlier: 6.639A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL E 17 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR E 33 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 45 " --> pdb=" O ILE E 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 87 removed outlier: 6.500A pdb=" N ILE E 105 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA E 126 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 3 removed outlier: 3.800A pdb=" N ALA F 66 " --> pdb=" O ARG F 2 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS F 35 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 40 through 46 removed outlier: 3.532A pdb=" N GLU F 40 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB2, first strand: chain 'H' and resid 73 through 76 Processing sheet with id=AB3, first strand: chain 'H' and resid 73 through 76 removed outlier: 6.859A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.824A pdb=" N ILE K 33 " --> pdb=" O LEU K 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 28 through 31 removed outlier: 13.961A pdb=" N GLU L 61 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N TYR L 94 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR L 63 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR L 96 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR L 65 " --> pdb=" O THR L 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 50 through 51 removed outlier: 4.963A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 36 through 41 removed outlier: 6.940A pdb=" N HIS Q 44 " --> pdb=" O TRP Q 72 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU Q 74 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N HIS Q 46 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ARG Q 76 " --> pdb=" O HIS Q 46 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER Q 71 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL Q 77 " --> pdb=" O VAL Q 57 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL Q 57 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLN Q 8 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLU Q 25 " --> pdb=" O GLN Q 8 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 51 through 55 removed outlier: 6.384A pdb=" N HIS C 68 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 54 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 66 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.646A pdb=" N GLU C 169 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'I' and resid 28 through 29 Processing sheet with id=AC4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.518A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.518A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 30 through 32 removed outlier: 5.192A pdb=" N LEU S 30 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N HIS S 51 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR S 32 " --> pdb=" O HIS S 51 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1259 hydrogen bonds 1960 hydrogen bond angles 0 basepair planarities 506 basepair parallelities 838 stacking parallelities Total time for adding SS restraints: 57.18 Time building geometry restraints manager: 30.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5805 1.31 - 1.44: 23199 1.44 - 1.58: 22055 1.58 - 1.71: 2725 1.71 - 1.85: 110 Bond restraints: 53894 Sorted by residual: bond pdb=" N9 A A 452 " pdb=" C4 A A 452 " ideal model delta sigma weight residual 1.374 1.295 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" P G A 388 " pdb=" OP2 G A 388 " ideal model delta sigma weight residual 1.485 1.409 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C VAL L 97 " pdb=" O VAL L 97 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.09e-02 8.42e+03 1.43e+01 bond pdb=" C5 G A 354 " pdb=" C6 G A 354 " ideal model delta sigma weight residual 1.419 1.344 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N GLN I 49 " pdb=" CA GLN I 49 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.24e+01 ... (remaining 53889 not shown) Histogram of bond angle deviations from ideal: 97.04 - 105.56: 8113 105.56 - 114.09: 34446 114.09 - 122.61: 27735 122.61 - 131.14: 9424 131.14 - 139.66: 521 Bond angle restraints: 80239 Sorted by residual: angle pdb=" C2' A A1396 " pdb=" C1' A A1396 " pdb=" N9 A A1396 " ideal model delta sigma weight residual 112.00 119.76 -7.76 1.50e+00 4.44e-01 2.68e+01 angle pdb=" C3' C A 328 " pdb=" O3' C A 328 " pdb=" P A A 329 " ideal model delta sigma weight residual 120.20 127.72 -7.52 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C2' G A 922 " pdb=" C1' G A 922 " pdb=" N9 G A 922 " ideal model delta sigma weight residual 114.00 106.90 7.10 1.50e+00 4.44e-01 2.24e+01 angle pdb=" O3' C A 328 " pdb=" C3' C A 328 " pdb=" C2' C A 328 " ideal model delta sigma weight residual 109.50 116.59 -7.09 1.50e+00 4.44e-01 2.24e+01 angle pdb=" O4' G A 752 " pdb=" C1' G A 752 " pdb=" N9 G A 752 " ideal model delta sigma weight residual 108.20 114.98 -6.78 1.50e+00 4.44e-01 2.04e+01 ... (remaining 80234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 30125 35.86 - 71.72: 3935 71.72 - 107.58: 424 107.58 - 143.45: 12 143.45 - 179.31: 12 Dihedral angle restraints: 34508 sinusoidal: 28189 harmonic: 6319 Sorted by residual: dihedral pdb=" O4' U A 610 " pdb=" C1' U A 610 " pdb=" N1 U A 610 " pdb=" C2 U A 610 " ideal model delta sinusoidal sigma weight residual -160.00 4.73 -164.73 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 63.97 136.03 1 1.50e+01 4.44e-03 7.34e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 74.29 125.71 1 1.50e+01 4.44e-03 6.76e+01 ... (remaining 34505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 8813 0.087 - 0.174: 1192 0.174 - 0.260: 164 0.260 - 0.347: 26 0.347 - 0.434: 3 Chirality restraints: 10198 Sorted by residual: chirality pdb=" C1' A A1396 " pdb=" O4' A A1396 " pdb=" C2' A A1396 " pdb=" N9 A A1396 " both_signs ideal model delta sigma weight residual False 2.46 2.02 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" C3' U A1528 " pdb=" C4' U A1528 " pdb=" O3' U A1528 " pdb=" C2' U A1528 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA VAL L 86 " pdb=" N VAL L 86 " pdb=" C VAL L 86 " pdb=" CB VAL L 86 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 10195 not shown) Planarity restraints: 4558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 922 " -0.078 2.00e-02 2.50e+03 3.45e-02 3.57e+01 pdb=" N9 G A 922 " 0.084 2.00e-02 2.50e+03 pdb=" C8 G A 922 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 922 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 922 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G A 922 " -0.012 2.00e-02 2.50e+03 pdb=" O6 G A 922 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G A 922 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G A 922 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G A 922 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 922 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G A 922 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 752 " 0.072 2.00e-02 2.50e+03 3.19e-02 3.05e+01 pdb=" N9 G A 752 " -0.076 2.00e-02 2.50e+03 pdb=" C8 G A 752 " -0.015 2.00e-02 2.50e+03 pdb=" N7 G A 752 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A 752 " 0.015 2.00e-02 2.50e+03 pdb=" C6 G A 752 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G A 752 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G A 752 " 0.010 2.00e-02 2.50e+03 pdb=" C2 G A 752 " -0.011 2.00e-02 2.50e+03 pdb=" N2 G A 752 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G A 752 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G A 752 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 380 " 0.073 2.00e-02 2.50e+03 3.03e-02 2.76e+01 pdb=" N9 G A 380 " -0.065 2.00e-02 2.50e+03 pdb=" C8 G A 380 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G A 380 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A 380 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 380 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G A 380 " 0.022 2.00e-02 2.50e+03 pdb=" N1 G A 380 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 380 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 380 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A 380 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G A 380 " -0.023 2.00e-02 2.50e+03 ... (remaining 4555 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 1181 2.56 - 3.15: 40297 3.15 - 3.73: 106795 3.73 - 4.32: 147156 4.32 - 4.90: 192204 Nonbonded interactions: 487633 Sorted by model distance: nonbonded pdb=" O2 C A 658 " pdb=" N2 G A 748 " model vdw 1.980 2.496 nonbonded pdb=" N2 G A 444 " pdb=" O2 C A 490 " model vdw 1.985 2.496 nonbonded pdb=" O2 U A 157 " pdb=" O6 G A 164 " model vdw 1.992 2.432 nonbonded pdb=" O2 U A 837 " pdb=" O6 G A 849 " model vdw 2.000 2.432 nonbonded pdb=" N2 G A 517 " pdb=" OP1 A A 533 " model vdw 2.012 2.520 ... (remaining 487628 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 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: 0.050 Extract box with map and model: 20.640 Check model and map are aligned: 0.900 Set scattering table: 0.450 Process input model: 183.890 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 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 : 0.014 0.107 53894 Z= 0.818 Angle : 1.068 13.161 80239 Z= 0.535 Chirality : 0.061 0.434 10198 Planarity : 0.007 0.051 4558 Dihedral : 24.110 179.308 30424 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.17), residues: 2166 helix: -1.03 (0.18), residues: 746 sheet: -1.79 (0.27), residues: 344 loop : -2.18 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP K 43 HIS 0.028 0.003 HIS O 45 PHE 0.039 0.003 PHE D 106 TYR 0.042 0.003 TYR D 74 ARG 0.023 0.002 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 21 MET cc_start: 0.0670 (tpp) cc_final: 0.0458 (tpp) REVERT: F 88 MET cc_start: 0.5585 (ptm) cc_final: 0.4884 (mtt) REVERT: G 30 MET cc_start: -0.1922 (ttt) cc_final: -0.2482 (ttt) REVERT: N 5 MET cc_start: -0.0806 (mmt) cc_final: -0.1474 (mmt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 2.0751 time to fit residues: 516.2140 Evaluate side-chains 169 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 284 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 329 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS F 55 HIS F 81 ASN O 34 GLN O 41 HIS I 49 GLN I 125 GLN N 61 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 53894 Z= 0.165 Angle : 0.639 11.861 80239 Z= 0.325 Chirality : 0.036 0.271 10198 Planarity : 0.005 0.042 4558 Dihedral : 24.586 179.078 26052 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.81 % Allowed : 10.82 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.91 (0.17), residues: 2166 helix: -0.29 (0.18), residues: 780 sheet: -1.28 (0.28), residues: 337 loop : -2.01 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 43 HIS 0.015 0.001 HIS O 45 PHE 0.016 0.001 PHE D 106 TYR 0.019 0.001 TYR L 94 ARG 0.010 0.001 ARG Q 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 88 MET cc_start: 0.5284 (ptm) cc_final: 0.5060 (mtt) REVERT: F 90 MET cc_start: 0.7003 (mmt) cc_final: 0.6303 (mmt) REVERT: H 2 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6596 (ttp) REVERT: G 30 MET cc_start: -0.1554 (ttt) cc_final: -0.2840 (tmt) REVERT: I 45 MET cc_start: 0.1780 (OUTLIER) cc_final: 0.1475 (pp-130) REVERT: M 80 MET cc_start: -0.1620 (mmt) cc_final: -0.3657 (ttt) REVERT: N 5 MET cc_start: -0.0602 (mmt) cc_final: -0.1181 (mmt) outliers start: 33 outliers final: 7 residues processed: 222 average time/residue: 1.8793 time to fit residues: 513.8360 Evaluate side-chains 183 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain I residue 45 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 274 optimal weight: 40.0000 chunk 224 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 356 optimal weight: 50.0000 chunk 294 optimal weight: 0.0370 chunk 327 optimal weight: 40.0000 chunk 112 optimal weight: 5.9990 chunk 264 optimal weight: 50.0000 overall best weight: 3.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN E 76 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN H 117 GLN L 95 HIS T 83 ASN N 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 53894 Z= 0.340 Angle : 0.692 11.751 80239 Z= 0.350 Chirality : 0.040 0.281 10198 Planarity : 0.005 0.065 4558 Dihedral : 24.464 179.021 26052 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.19 % Allowed : 14.01 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.73 (0.18), residues: 2166 helix: -0.08 (0.18), residues: 781 sheet: -1.20 (0.29), residues: 327 loop : -1.97 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 43 HIS 0.008 0.001 HIS Q 44 PHE 0.020 0.002 PHE F 8 TYR 0.019 0.002 TYR L 94 ARG 0.007 0.001 ARG T 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 90 MET cc_start: 0.7367 (mmt) cc_final: 0.6720 (mmt) REVERT: H 2 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6479 (ttt) REVERT: L 24 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: Q 25 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7148 (tp30) REVERT: G 30 MET cc_start: -0.1614 (ttt) cc_final: -0.2507 (tmt) REVERT: M 80 MET cc_start: -0.1607 (mmt) cc_final: -0.3423 (ttt) REVERT: N 5 MET cc_start: -0.0447 (mmt) cc_final: -0.1070 (mmt) outliers start: 58 outliers final: 22 residues processed: 208 average time/residue: 1.8948 time to fit residues: 484.9513 Evaluate side-chains 192 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain N residue 88 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 0.5980 chunk 248 optimal weight: 50.0000 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 331 optimal weight: 50.0000 chunk 350 optimal weight: 50.0000 chunk 173 optimal weight: 1.9990 chunk 314 optimal weight: 50.0000 chunk 94 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN E 96 GLN F 81 ASN H 117 GLN L 95 HIS ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 53894 Z= 0.240 Angle : 0.627 12.319 80239 Z= 0.319 Chirality : 0.037 0.267 10198 Planarity : 0.005 0.044 4558 Dihedral : 24.339 179.147 26052 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.75 % Allowed : 16.98 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.52 (0.18), residues: 2166 helix: 0.14 (0.19), residues: 778 sheet: -1.05 (0.30), residues: 325 loop : -1.90 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 43 HIS 0.006 0.001 HIS D 197 PHE 0.012 0.001 PHE D 106 TYR 0.018 0.002 TYR L 94 ARG 0.006 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 182 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 90 MET cc_start: 0.7358 (mmt) cc_final: 0.6577 (mmt) REVERT: H 2 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6369 (ttp) REVERT: G 30 MET cc_start: -0.1590 (ttt) cc_final: -0.2274 (tmt) REVERT: I 87 MET cc_start: 0.0858 (mpt) cc_final: 0.0652 (mpt) REVERT: M 80 MET cc_start: -0.1716 (mmt) cc_final: -0.3354 (ttt) REVERT: N 5 MET cc_start: -0.0612 (mmt) cc_final: -0.1433 (mmt) outliers start: 50 outliers final: 22 residues processed: 214 average time/residue: 1.8522 time to fit residues: 488.5593 Evaluate side-chains 193 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain N residue 88 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 261 optimal weight: 80.0000 chunk 144 optimal weight: 40.0000 chunk 299 optimal weight: 9.9990 chunk 242 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 179 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN E 60 GLN F 81 ASN H 117 GLN L 4 ASN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.096 53894 Z= 0.708 Angle : 0.928 13.079 80239 Z= 0.451 Chirality : 0.053 0.364 10198 Planarity : 0.007 0.093 4558 Dihedral : 24.474 179.224 26052 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 4.40 % Allowed : 17.31 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.79 (0.17), residues: 2166 helix: -0.20 (0.18), residues: 774 sheet: -0.99 (0.29), residues: 329 loop : -2.03 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 169 HIS 0.015 0.002 HIS L 71 PHE 0.019 0.002 PHE Q 36 TYR 0.030 0.003 TYR F 25 ARG 0.014 0.001 ARG P 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 175 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6802 (mm110) REVERT: F 90 MET cc_start: 0.7568 (mmt) cc_final: 0.6717 (mmt) REVERT: H 2 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6321 (ttt) REVERT: L 24 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: Q 25 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7167 (tp30) REVERT: G 30 MET cc_start: -0.1614 (ttt) cc_final: -0.2202 (tmt) REVERT: I 87 MET cc_start: 0.0859 (mpt) cc_final: 0.0415 (mpt) REVERT: M 80 MET cc_start: -0.1797 (mmt) cc_final: -0.3450 (ttt) REVERT: N 5 MET cc_start: -0.0698 (mmt) cc_final: -0.1608 (mmt) REVERT: S 65 MET cc_start: 0.0194 (OUTLIER) cc_final: -0.0093 (tpt) outliers start: 80 outliers final: 37 residues processed: 225 average time/residue: 1.8047 time to fit residues: 506.5054 Evaluate side-chains 204 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 65 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 1.9990 chunk 315 optimal weight: 50.0000 chunk 69 optimal weight: 0.9990 chunk 206 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 291 optimal weight: 50.0000 chunk 162 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 151 GLN E 18 ASN F 81 ASN L 4 ASN O 45 HIS ** S 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53894 Z= 0.173 Angle : 0.609 12.950 80239 Z= 0.309 Chirality : 0.035 0.269 10198 Planarity : 0.004 0.038 4558 Dihedral : 24.288 179.398 26052 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.02 % Allowed : 19.84 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.42 (0.18), residues: 2166 helix: 0.21 (0.19), residues: 783 sheet: -0.87 (0.29), residues: 341 loop : -1.89 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 169 HIS 0.006 0.001 HIS D 197 PHE 0.014 0.001 PHE F 8 TYR 0.020 0.001 TYR F 25 ARG 0.005 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 192 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6274 (ttp) REVERT: G 30 MET cc_start: -0.1500 (ttt) cc_final: -0.1934 (tmt) REVERT: M 80 MET cc_start: -0.1609 (mmt) cc_final: -0.3328 (ttt) REVERT: N 5 MET cc_start: -0.0594 (mmt) cc_final: -0.1457 (mmt) REVERT: S 65 MET cc_start: 0.0135 (tpt) cc_final: -0.0098 (tpt) outliers start: 55 outliers final: 30 residues processed: 234 average time/residue: 1.8919 time to fit residues: 549.3399 Evaluate side-chains 207 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain T residue 84 LYS Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain S residue 22 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 256 optimal weight: 50.0000 chunk 198 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 349 optimal weight: 40.0000 chunk 218 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN L 4 ASN T 83 ASN C 101 ASN S 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 53894 Z= 0.494 Angle : 0.772 12.615 80239 Z= 0.383 Chirality : 0.045 0.312 10198 Planarity : 0.006 0.074 4558 Dihedral : 24.327 179.366 26052 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.68 % Allowed : 20.22 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2166 helix: 0.09 (0.19), residues: 787 sheet: -0.89 (0.29), residues: 321 loop : -1.91 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 169 HIS 0.009 0.002 HIS L 71 PHE 0.023 0.002 PHE F 8 TYR 0.021 0.002 TYR L 116 ARG 0.008 0.001 ARG P 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 178 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 177 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5192 (mtp) REVERT: H 2 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6376 (ttt) REVERT: L 24 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: G 117 LEU cc_start: -0.1780 (OUTLIER) cc_final: -0.2006 (pt) REVERT: M 80 MET cc_start: -0.1668 (mmt) cc_final: -0.3268 (ttt) REVERT: N 5 MET cc_start: -0.0677 (mmt) cc_final: -0.1481 (mmt) outliers start: 67 outliers final: 40 residues processed: 225 average time/residue: 1.8166 time to fit residues: 506.3400 Evaluate side-chains 214 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain T residue 84 LYS Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain S residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 238 optimal weight: 50.0000 chunk 172 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 275 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN F 81 ASN L 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 53894 Z= 0.153 Angle : 0.595 13.385 80239 Z= 0.301 Chirality : 0.034 0.269 10198 Planarity : 0.004 0.051 4558 Dihedral : 24.185 179.444 26052 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.58 % Allowed : 22.09 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2166 helix: 0.40 (0.19), residues: 785 sheet: -0.79 (0.29), residues: 332 loop : -1.84 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 169 HIS 0.006 0.001 HIS D 197 PHE 0.018 0.001 PHE F 8 TYR 0.015 0.001 TYR B 21 ARG 0.006 0.000 ARG E 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 ILE cc_start: 0.3897 (OUTLIER) cc_final: 0.3472 (tp) REVERT: F 90 MET cc_start: 0.7241 (mmt) cc_final: 0.6562 (mmt) REVERT: H 2 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6287 (ttp) REVERT: M 80 MET cc_start: -0.1552 (mmt) cc_final: -0.3479 (ttt) REVERT: N 5 MET cc_start: -0.0842 (mmt) cc_final: -0.1385 (mmt) outliers start: 47 outliers final: 25 residues processed: 232 average time/residue: 1.9029 time to fit residues: 547.1790 Evaluate side-chains 212 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain S residue 22 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 40.0000 chunk 335 optimal weight: 4.9990 chunk 305 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 256 optimal weight: 50.0000 chunk 100 optimal weight: 7.9990 chunk 294 optimal weight: 0.4980 chunk 308 optimal weight: 5.9990 chunk 324 optimal weight: 0.0980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN L 4 ASN O 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 53894 Z= 0.327 Angle : 0.676 12.962 80239 Z= 0.339 Chirality : 0.039 0.327 10198 Planarity : 0.005 0.051 4558 Dihedral : 24.191 179.506 26052 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.53 % Allowed : 22.36 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2166 helix: 0.34 (0.19), residues: 783 sheet: -0.81 (0.30), residues: 321 loop : -1.76 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 169 HIS 0.007 0.001 HIS D 197 PHE 0.028 0.001 PHE F 8 TYR 0.018 0.002 TYR L 94 ARG 0.017 0.000 ARG Q 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 184 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 90 MET cc_start: 0.7459 (mmt) cc_final: 0.6798 (mmt) REVERT: H 2 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6388 (ttt) REVERT: M 80 MET cc_start: -0.1505 (mmt) cc_final: -0.3438 (ttt) REVERT: N 5 MET cc_start: -0.0876 (mmt) cc_final: -0.1415 (mmt) outliers start: 46 outliers final: 33 residues processed: 216 average time/residue: 1.8538 time to fit residues: 493.7662 Evaluate side-chains 215 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain S residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 40.0000 chunk 344 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 239 optimal weight: 50.0000 chunk 361 optimal weight: 50.0000 chunk 332 optimal weight: 50.0000 chunk 287 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN H 117 GLN L 4 ASN T 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 53894 Z= 0.491 Angle : 0.782 12.918 80239 Z= 0.388 Chirality : 0.045 0.324 10198 Planarity : 0.006 0.074 4558 Dihedral : 24.318 179.527 26052 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.69 % Allowed : 22.47 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2166 helix: 0.14 (0.19), residues: 779 sheet: -0.81 (0.30), residues: 316 loop : -1.79 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 169 HIS 0.011 0.002 HIS L 71 PHE 0.021 0.002 PHE F 8 TYR 0.023 0.002 TYR L 116 ARG 0.016 0.001 ARG Q 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 ILE cc_start: 0.3815 (OUTLIER) cc_final: 0.3297 (tp) REVERT: F 90 MET cc_start: 0.7415 (mmt) cc_final: 0.6741 (mmt) REVERT: H 2 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6336 (ttt) REVERT: O 34 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: M 80 MET cc_start: -0.1524 (mmt) cc_final: -0.3358 (ttt) REVERT: N 5 MET cc_start: -0.0842 (mmt) cc_final: -0.1171 (mpt) REVERT: S 43 MET cc_start: -0.1575 (ptt) cc_final: -0.2042 (pmt) outliers start: 49 outliers final: 35 residues processed: 213 average time/residue: 1.8413 time to fit residues: 485.6305 Evaluate side-chains 211 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain S residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 40.0000 chunk 306 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 265 optimal weight: 50.0000 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN H 117 GLN L 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.189515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.168152 restraints weight = 79799.735| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 0.66 r_work: 0.4242 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4203 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 53894 Z= 0.384 Angle : 0.714 13.277 80239 Z= 0.358 Chirality : 0.041 0.289 10198 Planarity : 0.005 0.069 4558 Dihedral : 24.274 179.919 26052 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.36 % Allowed : 22.91 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2166 helix: 0.12 (0.18), residues: 791 sheet: -0.83 (0.30), residues: 314 loop : -1.82 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 169 HIS 0.008 0.001 HIS L 95 PHE 0.012 0.001 PHE Q 36 TYR 0.019 0.002 TYR L 116 ARG 0.015 0.001 ARG Q 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10568.61 seconds wall clock time: 197 minutes 8.75 seconds (11828.75 seconds total)