Starting phenix.real_space_refine (version: dev) on Thu Dec 22 16:30:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/12_2022/7oe0_12856.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/12_2022/7oe0_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_12856/12_2022/7oe0_12856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/12_2022/7oe0_12856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/12_2022/7oe0_12856.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe0_12856/12_2022/7oe0_12856.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 26.14, per 1000 atoms: 0.52 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: 28.12 Conformation dependent library (CDL) restraints added in 2.8 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: 24.64 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: 64.59 Time building geometry restraints manager: 29.71 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: 27633 35.86 - 71.72: 1245 71.72 - 107.58: 126 107.58 - 143.45: 12 143.45 - 179.31: 12 Dihedral angle restraints: 29028 sinusoidal: 22709 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 29025 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 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. 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: 2.870 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: 0.030 Extract box with map and model: 21.410 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.450 Process input model: 188.680 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 227.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 16.905 179.308 24944 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 2.0493 time to fit residues: 514.6404 Evaluate side-chains 169 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9145 ------------------------------------------------------------------------------- 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 O 34 GLN O 41 HIS I 49 GLN I 125 GLN N 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 53894 Z= 0.166 Angle : 0.640 12.205 80239 Z= 0.325 Chirality : 0.036 0.273 10198 Planarity : 0.005 0.056 4558 Dihedral : 16.262 179.086 20572 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer Outliers : 1.76 % 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: -0.32 (0.18), residues: 784 sheet: -1.28 (0.28), residues: 337 loop : -2.01 (0.18), residues: 1045 *********************** 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 239 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 3.100 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 outliers start: 32 outliers final: 7 residues processed: 221 average time/residue: 1.7433 time to fit residues: 480.9599 Evaluate side-chains 185 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 3.170 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.7716 time to fit residues: 7.6884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 274 optimal weight: 40.0000 chunk 224 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 330 optimal weight: 50.0000 chunk 356 optimal weight: 50.0000 chunk 294 optimal weight: 6.9990 chunk 327 optimal weight: 50.0000 chunk 112 optimal weight: 6.9990 chunk 264 optimal weight: 50.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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** H 117 GLN L 95 HIS T 83 ASN N 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.063 53894 Z= 0.454 Angle : 0.761 11.768 80239 Z= 0.380 Chirality : 0.044 0.309 10198 Planarity : 0.006 0.071 4558 Dihedral : 16.294 179.037 20572 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer Outliers : 3.30 % 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: -1.83 (0.18), residues: 2166 helix: -0.18 (0.18), residues: 781 sheet: -1.23 (0.29), residues: 319 loop : -2.01 (0.18), residues: 1066 *********************** 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 230 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 170 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 23 residues processed: 206 average time/residue: 1.7648 time to fit residues: 452.5313 Evaluate side-chains 188 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 3.124 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 12 residues processed: 11 average time/residue: 1.4210 time to fit residues: 23.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 10.0000 chunk 248 optimal weight: 50.0000 chunk 171 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 331 optimal weight: 50.0000 chunk 350 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 314 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 H 117 GLN L 95 HIS ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1875 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= 0.176 Angle : 0.601 12.046 80239 Z= 0.306 Chirality : 0.035 0.270 10198 Planarity : 0.004 0.039 4558 Dihedral : 15.939 179.306 20572 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 3.02 % 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: -1.48 (0.18), residues: 2166 helix: 0.20 (0.19), residues: 777 sheet: -1.04 (0.30), residues: 325 loop : -1.89 (0.18), residues: 1064 *********************** 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 243 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 3.131 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 outliers start: 55 outliers final: 21 residues processed: 224 average time/residue: 1.8191 time to fit residues: 504.5597 Evaluate side-chains 192 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 1.0760 time to fit residues: 10.8827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 50.0000 chunk 199 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 261 optimal weight: 70.0000 chunk 144 optimal weight: 40.0000 chunk 299 optimal weight: 8.9990 chunk 242 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 179 optimal weight: 6.9990 chunk 314 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 H 3 GLN H 117 GLN L 4 ASN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.092 53894 Z= 0.694 Angle : 0.909 11.963 80239 Z= 0.443 Chirality : 0.053 0.366 10198 Planarity : 0.007 0.090 4558 Dihedral : 16.367 179.478 20572 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer Outliers : 4.40 % 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: -1.75 (0.18), residues: 2166 helix: -0.13 (0.18), residues: 773 sheet: -1.08 (0.29), residues: 321 loop : -1.97 (0.18), residues: 1072 *********************** 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 261 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 181 time to evaluate : 3.350 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 outliers start: 80 outliers final: 40 residues processed: 230 average time/residue: 1.7104 time to fit residues: 496.7181 Evaluate side-chains 205 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 26 residues processed: 14 average time/residue: 1.1108 time to fit residues: 25.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 0.8980 chunk 315 optimal weight: 50.0000 chunk 69 optimal weight: 0.9990 chunk 206 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 351 optimal weight: 20.0000 chunk 291 optimal weight: 0.0980 chunk 162 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN H 3 GLN L 4 ASN O 45 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 53894 Z= 0.145 Angle : 0.602 13.087 80239 Z= 0.305 Chirality : 0.034 0.272 10198 Planarity : 0.004 0.038 4558 Dihedral : 15.889 179.675 20572 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 3.85 % 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: -1.36 (0.18), residues: 2166 helix: 0.31 (0.19), residues: 780 sheet: -0.93 (0.29), residues: 344 loop : -1.86 (0.19), residues: 1042 *********************** 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 265 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 195 time to evaluate : 3.308 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 outliers start: 70 outliers final: 35 residues processed: 249 average time/residue: 1.7539 time to fit residues: 544.5246 Evaluate side-chains 215 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 4 average time/residue: 0.7698 time to fit residues: 8.1656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 256 optimal weight: 60.0000 chunk 198 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 349 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** L 4 ASN L 74 GLN T 83 ASN C 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 53894 Z= 0.423 Angle : 0.732 13.642 80239 Z= 0.365 Chirality : 0.042 0.302 10198 Planarity : 0.006 0.070 4558 Dihedral : 15.983 179.709 20572 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2166 helix: 0.09 (0.19), residues: 784 sheet: -0.90 (0.30), residues: 321 loop : -1.87 (0.18), residues: 1061 *********************** 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 : 3.505 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 outliers start: 67 outliers final: 36 residues processed: 222 average time/residue: 1.6636 time to fit residues: 463.6622 Evaluate side-chains 206 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 3.126 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 1.0319 time to fit residues: 10.6158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 6.9990 chunk 139 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 238 optimal weight: 50.0000 chunk 172 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 275 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 E 60 GLN H 3 GLN H 117 GLN L 4 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 53894 Z= 0.164 Angle : 0.596 13.259 80239 Z= 0.302 Chirality : 0.034 0.327 10198 Planarity : 0.004 0.053 4558 Dihedral : 15.729 179.836 20572 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer Outliers : 2.97 % 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: -1.31 (0.18), residues: 2166 helix: 0.32 (0.19), residues: 780 sheet: -0.86 (0.29), residues: 335 loop : -1.81 (0.19), residues: 1051 *********************** 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 248 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 3.239 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 outliers start: 54 outliers final: 34 residues processed: 231 average time/residue: 1.8513 time to fit residues: 532.7170 Evaluate side-chains 220 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 29 residues processed: 5 average time/residue: 1.3771 time to fit residues: 12.6298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 50.0000 chunk 335 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 256 optimal weight: 50.0000 chunk 100 optimal weight: 9.9990 chunk 294 optimal weight: 30.0000 chunk 308 optimal weight: 8.9990 chunk 324 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 L 4 ASN O 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.072 53894 Z= 0.628 Angle : 0.867 13.461 80239 Z= 0.423 Chirality : 0.050 0.357 10198 Planarity : 0.006 0.078 4558 Dihedral : 16.135 179.919 20572 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer Outliers : 3.13 % 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: -1.49 (0.18), residues: 2166 helix: 0.04 (0.19), residues: 777 sheet: -0.89 (0.30), residues: 318 loop : -1.81 (0.19), residues: 1071 *********************** 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 237 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 180 time to evaluate : 3.300 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 outliers start: 57 outliers final: 37 residues processed: 220 average time/residue: 1.7080 time to fit residues: 474.1162 Evaluate side-chains 214 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 3.458 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 7 average time/residue: 0.6391 time to fit residues: 11.1669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 30.0000 chunk 344 optimal weight: 8.9990 chunk 210 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 239 optimal weight: 50.0000 chunk 361 optimal weight: 30.0000 chunk 332 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 222 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 H 3 GLN L 4 ASN O 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 53894 Z= 0.195 Angle : 0.621 13.804 80239 Z= 0.313 Chirality : 0.036 0.503 10198 Planarity : 0.004 0.040 4558 Dihedral : 15.788 179.937 20572 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 2.14 % 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: 0.32 (0.19), residues: 782 sheet: -0.79 (0.30), residues: 318 loop : -1.75 (0.19), residues: 1066 ********************** 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 230 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 3.418 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 outliers start: 39 outliers final: 30 residues processed: 224 average time/residue: 1.8150 time to fit residues: 506.5911 Evaluate side-chains 213 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 3.216 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 2 average time/residue: 0.5897 time to fit residues: 5.4774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 88 optimal weight: 8.9990 chunk 265 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 288 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN L 4 ASN T 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.189920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.168881 restraints weight = 80623.576| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 0.60 r_work: 0.4249 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4217 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2452 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= 0.321 Angle : 0.675 13.871 80239 Z= 0.339 Chirality : 0.039 0.481 10198 Planarity : 0.005 0.052 4558 Dihedral : 15.808 179.865 20572 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer Outliers : 2.14 % 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: -1.28 (0.18), residues: 2166 helix: 0.25 (0.19), residues: 786 sheet: -0.78 (0.30), residues: 318 loop : -1.74 (0.19), residues: 1062 =============================================================================== Job complete usr+sys time: 10155.75 seconds wall clock time: 185 minutes 2.59 seconds (11102.59 seconds total)