Starting phenix.real_space_refine on Tue Mar 12 18:00:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/03_2024/8c90_16497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/03_2024/8c90_16497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/03_2024/8c90_16497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/03_2024/8c90_16497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/03_2024/8c90_16497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/03_2024/8c90_16497.pdb" } resolution = 3.15 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= 0.008 sd= 0.110 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 2219 5.49 5 S 48 5.16 5 C 31957 2.51 5 N 12080 2.21 5 O 18422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 64726 Number of models: 1 Model: "" Number of chains: 22 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 45129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2100, 45129 Classifications: {'RNA': 2100} Modifications used: {'rna2p_pur': 201, 'rna2p_pyr': 112, 'rna3p_pur': 1028, 'rna3p_pyr': 759} Link IDs: {'rna2p': 313, 'rna3p': 1786} Chain breaks: 8 Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1348 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1512 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 824 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 108} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 820 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "2" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 349 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 528 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 25.51, per 1000 atoms: 0.39 Number of scatterers: 64726 At special positions: 0 Unit cell: (182.5, 236.25, 202.5, 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 48 16.00 P 2219 15.00 O 18422 8.00 N 12080 7.00 C 31957 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: 27.55 Conformation dependent library (CDL) restraints added in 3.0 seconds 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 29 sheets defined 34.2% alpha, 19.8% beta 733 base pairs and 1048 stacking pairs defined. Time for finding SS restraints: 26.30 Creating SS restraints... Processing helix chain 'V' and resid 13 through 23 removed outlier: 3.774A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.326A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.613A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.037A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 4.065A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.380A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 4.129A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 136 removed outlier: 4.537A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.634A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.179A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.606A pdb=" N ARG P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.899A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.127A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.589A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.655A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.697A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'T' and resid 3 through 10 Processing helix chain 'T' and resid 17 through 28 Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.508A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.027A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 17 Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 Processing helix chain 'O' and resid 3 through 21 removed outlier: 4.292A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.947A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 20 removed outlier: 4.594A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.510A pdb=" N GLN F 26 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 23 through 27' Processing helix chain 'F' and resid 41 through 44 removed outlier: 3.765A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 45 through 60 removed outlier: 4.349A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.880A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 137 removed outlier: 3.802A pdb=" N PHE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 134 through 137' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.887A pdb=" N VAL F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'V' and resid 3 through 4 removed outlier: 5.525A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 169 through 175 removed outlier: 6.016A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.446A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.583A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.773A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.976A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.624A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.569A pdb=" N LEU K 8 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.902A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 74 through 78 removed outlier: 3.645A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 121 through 123 removed outlier: 5.812A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.458A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 11 through 15 removed outlier: 7.204A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.750A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.090A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 3 through 10 removed outlier: 3.620A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AB9, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.792A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.519A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS U 23 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP U 80 " --> pdb=" O ILE U 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.646A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AC5, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC6, first strand: chain 'O' and resid 47 through 52 removed outlier: 4.332A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU O 26 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.726A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU F 35 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC9, first strand: chain 'Z' and resid 35 through 38 removed outlier: 3.880A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.926A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 26 through 27 removed outlier: 6.169A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1869 hydrogen bonds 2992 hydrogen bond angles 0 basepair planarities 733 basepair parallelities 1048 stacking parallelities Total time for adding SS restraints: 79.57 Time building geometry restraints manager: 29.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10573 1.33 - 1.45: 29482 1.45 - 1.57: 26079 1.57 - 1.69: 4428 1.69 - 1.81: 91 Bond restraints: 70653 Sorted by residual: bond pdb=" N MET T 1 " pdb=" CA MET T 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET N 1 " pdb=" CA MET N 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 70648 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.23: 13511 107.23 - 113.92: 44307 113.92 - 120.61: 25623 120.61 - 127.29: 18135 127.29 - 133.98: 4828 Bond angle restraints: 106404 Sorted by residual: angle pdb=" N GLU P 33 " pdb=" CA GLU P 33 " pdb=" C GLU P 33 " ideal model delta sigma weight residual 110.61 115.26 -4.65 1.25e+00 6.40e-01 1.38e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 127.93 -6.23 1.80e+00 3.09e-01 1.20e+01 angle pdb=" CA GLU P 33 " pdb=" C GLU P 33 " pdb=" N SER P 35 " ideal model delta sigma weight residual 116.74 121.04 -4.30 1.42e+00 4.96e-01 9.17e+00 angle pdb=" C GLU P 33 " pdb=" N SER P 35 " pdb=" CA SER P 35 " ideal model delta sigma weight residual 121.70 127.05 -5.35 1.80e+00 3.09e-01 8.84e+00 angle pdb=" CA GLY L 28 " pdb=" C GLY L 28 " pdb=" N LYS L 29 " ideal model delta sigma weight residual 114.48 117.90 -3.42 1.19e+00 7.06e-01 8.25e+00 ... (remaining 106399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 39572 34.41 - 68.83: 5060 68.83 - 103.24: 611 103.24 - 137.66: 17 137.66 - 172.07: 7 Dihedral angle restraints: 45267 sinusoidal: 39056 harmonic: 6211 Sorted by residual: dihedral pdb=" O4' C A1675 " pdb=" C1' C A1675 " pdb=" N1 C A1675 " pdb=" C2 C A1675 " ideal model delta sinusoidal sigma weight residual 200.00 49.01 150.99 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual 232.00 61.15 170.85 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 35.67 -163.67 1 1.70e+01 3.46e-03 6.51e+01 ... (remaining 45264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 10766 0.031 - 0.062: 2511 0.062 - 0.094: 226 0.094 - 0.125: 187 0.125 - 0.156: 26 Chirality restraints: 13716 Sorted by residual: chirality pdb=" CA VAL R 51 " pdb=" N VAL R 51 " pdb=" C VAL R 51 " pdb=" CB VAL R 51 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE T 2 " pdb=" N ILE T 2 " pdb=" C ILE T 2 " pdb=" CB ILE T 2 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE S 103 " pdb=" N ILE S 103 " pdb=" C ILE S 103 " pdb=" CB ILE S 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 13713 not shown) Planarity restraints: 5189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 418 " 0.004 2.00e-02 2.50e+03 1.82e-02 7.49e+00 pdb=" N1 C A 418 " 0.002 2.00e-02 2.50e+03 pdb=" C2 C A 418 " -0.045 2.00e-02 2.50e+03 pdb=" O2 C A 418 " 0.024 2.00e-02 2.50e+03 pdb=" N3 C A 418 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C A 418 " -0.013 2.00e-02 2.50e+03 pdb=" N4 C A 418 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C A 418 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A 418 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 903 " 0.008 2.00e-02 2.50e+03 1.65e-02 6.10e+00 pdb=" N1 C A 903 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C A 903 " -0.041 2.00e-02 2.50e+03 pdb=" O2 C A 903 " 0.022 2.00e-02 2.50e+03 pdb=" N3 C A 903 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C A 903 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C A 903 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C A 903 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C A 903 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2264 " 0.006 2.00e-02 2.50e+03 1.52e-02 5.23e+00 pdb=" N1 C A2264 " -0.005 2.00e-02 2.50e+03 pdb=" C2 C A2264 " -0.038 2.00e-02 2.50e+03 pdb=" O2 C A2264 " 0.023 2.00e-02 2.50e+03 pdb=" N3 C A2264 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C A2264 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C A2264 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C A2264 " 0.007 2.00e-02 2.50e+03 pdb=" C6 C A2264 " 0.002 2.00e-02 2.50e+03 ... (remaining 5186 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 380 2.47 - 3.08: 41191 3.08 - 3.69: 120566 3.69 - 4.29: 173139 4.29 - 4.90: 240223 Nonbonded interactions: 575499 Sorted by model distance: nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 1.866 2.440 nonbonded pdb=" O2' A A 905 " pdb=" O4' U A 906 " model vdw 1.917 2.440 nonbonded pdb=" OP2 U A 369 " pdb=" O2' U A 403 " model vdw 1.934 2.440 nonbonded pdb=" O2' C A1462 " pdb=" O2' G A2702 " model vdw 1.946 2.440 nonbonded pdb=" O2' U A 534 " pdb=" OD2 ASP Q 48 " model vdw 1.955 2.440 ... (remaining 575494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 8.300 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 205.520 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.160 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 220.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 70653 Z= 0.097 Angle : 0.383 6.690 106404 Z= 0.202 Chirality : 0.027 0.156 13716 Planarity : 0.002 0.030 5189 Dihedral : 22.688 172.073 41253 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 2135 helix: 2.22 (0.22), residues: 662 sheet: 0.02 (0.27), residues: 414 loop : -0.80 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 60 HIS 0.004 0.001 HIS J 77 PHE 0.011 0.001 PHE S 75 TYR 0.015 0.001 TYR J 75 ARG 0.005 0.000 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 200 ASP cc_start: 0.7722 (m-30) cc_final: 0.7462 (m-30) REVERT: J 84 ILE cc_start: 0.7289 (tt) cc_final: 0.7055 (mt) REVERT: K 115 ILE cc_start: 0.6993 (mm) cc_final: 0.6689 (mp) REVERT: S 2 GLU cc_start: 0.6414 (tp30) cc_final: 0.6106 (tp30) REVERT: T 54 GLU cc_start: 0.6296 (pp20) cc_final: 0.5997 (pp20) REVERT: T 87 LEU cc_start: 0.6644 (mt) cc_final: 0.6354 (mp) REVERT: O 98 GLN cc_start: 0.6382 (mm-40) cc_final: 0.5951 (mm-40) REVERT: O 100 HIS cc_start: 0.4826 (p90) cc_final: 0.4217 (p90) REVERT: F 37 MET cc_start: 0.5052 (mmt) cc_final: 0.4640 (mmm) REVERT: F 96 TRP cc_start: 0.5544 (m100) cc_final: 0.5343 (m100) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.6157 time to fit residues: 306.2402 Evaluate side-chains 191 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 30.0000 chunk 338 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 205 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 30.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 62 GLN J 76 HIS J 132 HIS K 5 GLN L 35 HIS P 9 GLN S 15 GLN T 92 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 98 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 70653 Z= 0.524 Angle : 0.778 9.952 106404 Z= 0.382 Chirality : 0.041 0.416 13716 Planarity : 0.006 0.060 5189 Dihedral : 23.417 178.971 36986 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.74 % Rotamer: Outliers : 2.08 % Allowed : 8.62 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2135 helix: 0.69 (0.20), residues: 673 sheet: -0.29 (0.27), residues: 400 loop : -1.14 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP P 30 HIS 0.011 0.003 HIS N 3 PHE 0.032 0.003 PHE S 75 TYR 0.038 0.004 TYR V 31 ARG 0.013 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 79 ARG cc_start: 0.7228 (mmm160) cc_final: 0.6924 (mmm160) REVERT: J 84 ILE cc_start: 0.7677 (tt) cc_final: 0.7326 (mt) REVERT: J 92 MET cc_start: 0.7929 (tpp) cc_final: 0.7407 (mmm) REVERT: K 1 MET cc_start: 0.3875 (ttm) cc_final: 0.3671 (ttm) REVERT: K 115 ILE cc_start: 0.6989 (mm) cc_final: 0.6728 (mp) REVERT: T 1 MET cc_start: 0.7129 (tmm) cc_final: 0.5061 (pmm) REVERT: T 32 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8187 (pp) REVERT: T 54 GLU cc_start: 0.7007 (pp20) cc_final: 0.6744 (pp20) REVERT: O 8 ILE cc_start: 0.7862 (mm) cc_final: 0.7659 (mm) REVERT: O 98 GLN cc_start: 0.7061 (mm110) cc_final: 0.6504 (mm-40) REVERT: O 100 HIS cc_start: 0.4556 (p90) cc_final: 0.4289 (p90) outliers start: 37 outliers final: 23 residues processed: 233 average time/residue: 0.6775 time to fit residues: 272.4195 Evaluate side-chains 203 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 326 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 393 optimal weight: 20.0000 chunk 424 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 389 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 315 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 12 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 70653 Z= 0.149 Angle : 0.495 11.873 106404 Z= 0.252 Chirality : 0.029 0.211 13716 Planarity : 0.004 0.043 5189 Dihedral : 23.291 175.584 36986 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 2.08 % Allowed : 12.34 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2135 helix: 1.23 (0.21), residues: 664 sheet: -0.38 (0.26), residues: 423 loop : -0.97 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P 30 HIS 0.004 0.001 HIS U 44 PHE 0.024 0.001 PHE S 75 TYR 0.014 0.001 TYR F 127 ARG 0.009 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 200 ASP cc_start: 0.7913 (m-30) cc_final: 0.7666 (m-30) REVERT: J 92 MET cc_start: 0.7704 (tpp) cc_final: 0.7402 (mmm) REVERT: K 25 LEU cc_start: 0.7831 (mm) cc_final: 0.7576 (mm) REVERT: K 115 ILE cc_start: 0.6872 (mm) cc_final: 0.6631 (mp) REVERT: L 79 LEU cc_start: 0.8866 (mt) cc_final: 0.8666 (mt) REVERT: T 1 MET cc_start: 0.6865 (tmm) cc_final: 0.5075 (pmm) REVERT: O 26 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7120 (tp) REVERT: O 98 GLN cc_start: 0.6910 (mm110) cc_final: 0.6504 (mm-40) REVERT: O 100 HIS cc_start: 0.4496 (p90) cc_final: 0.4286 (p90) outliers start: 37 outliers final: 23 residues processed: 234 average time/residue: 0.6075 time to fit residues: 244.9120 Evaluate side-chains 207 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain F residue 140 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 203 optimal weight: 50.0000 chunk 43 optimal weight: 10.0000 chunk 187 optimal weight: 40.0000 chunk 263 optimal weight: 10.0000 chunk 394 optimal weight: 50.0000 chunk 417 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 8.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 9 GLN P 74 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 GLN O 38 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 70653 Z= 0.427 Angle : 0.702 9.151 106404 Z= 0.348 Chirality : 0.038 0.234 13716 Planarity : 0.005 0.060 5189 Dihedral : 23.473 177.540 36986 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.15 % Favored : 91.80 % Rotamer: Outliers : 4.73 % Allowed : 14.31 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2135 helix: 0.64 (0.20), residues: 667 sheet: -0.76 (0.25), residues: 438 loop : -1.18 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 30 HIS 0.010 0.002 HIS Z 19 PHE 0.029 0.002 PHE S 75 TYR 0.020 0.002 TYR S 38 ARG 0.018 0.001 ARG V 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 195 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 116 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: E 176 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7162 (p0) REVERT: J 92 MET cc_start: 0.7994 (tpp) cc_final: 0.7335 (mmm) REVERT: K 115 ILE cc_start: 0.6920 (mm) cc_final: 0.6690 (mp) REVERT: R 55 ASP cc_start: 0.6077 (p0) cc_final: 0.5819 (m-30) REVERT: S 66 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7368 (tt) REVERT: T 1 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.5463 (pmm) REVERT: T 32 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8163 (pp) REVERT: O 26 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7108 (tp) REVERT: F 121 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5189 (t80) outliers start: 84 outliers final: 53 residues processed: 251 average time/residue: 0.6326 time to fit residues: 276.8511 Evaluate side-chains 241 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 181 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 79 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 356 optimal weight: 0.9980 chunk 288 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN P 74 GLN O 38 GLN F 36 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 70653 Z= 0.292 Angle : 0.582 8.656 106404 Z= 0.294 Chirality : 0.034 0.227 13716 Planarity : 0.004 0.058 5189 Dihedral : 23.417 177.236 36986 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 4.51 % Allowed : 15.77 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2135 helix: 0.79 (0.21), residues: 672 sheet: -0.77 (0.25), residues: 437 loop : -1.22 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 30 HIS 0.006 0.001 HIS Z 19 PHE 0.024 0.002 PHE S 75 TYR 0.014 0.002 TYR S 38 ARG 0.010 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 194 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 31 TYR cc_start: 0.5982 (p90) cc_final: 0.5636 (p90) REVERT: V 50 MET cc_start: 0.1103 (mtm) cc_final: 0.0868 (mtm) REVERT: D 39 ASP cc_start: 0.7799 (p0) cc_final: 0.7571 (p0) REVERT: E 153 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7012 (mm) REVERT: E 176 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.7020 (p0) REVERT: J 1 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6950 (ptp) REVERT: J 92 MET cc_start: 0.7859 (tpp) cc_final: 0.7300 (mmm) REVERT: K 115 ILE cc_start: 0.6879 (mm) cc_final: 0.6657 (mp) REVERT: R 55 ASP cc_start: 0.6216 (p0) cc_final: 0.5934 (m-30) REVERT: S 66 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7246 (tt) REVERT: S 95 ARG cc_start: 0.5706 (tpt170) cc_final: 0.4300 (ttm170) REVERT: T 1 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.5472 (pmm) REVERT: T 32 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8082 (pp) REVERT: O 26 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7224 (tp) REVERT: F 121 PHE cc_start: 0.5616 (OUTLIER) cc_final: 0.5207 (t80) outliers start: 80 outliers final: 47 residues processed: 245 average time/residue: 0.5990 time to fit residues: 253.5693 Evaluate side-chains 239 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 184 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain W residue 79 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 50.0000 chunk 376 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 138 optimal weight: 50.0000 chunk 219 optimal weight: 1.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN P 74 GLN U 52 ASN 2 16 HIS O 38 GLN F 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 70653 Z= 0.363 Angle : 0.644 11.504 106404 Z= 0.323 Chirality : 0.036 0.377 13716 Planarity : 0.005 0.053 5189 Dihedral : 23.475 177.043 36986 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.73 % Allowed : 16.79 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 2135 helix: 0.58 (0.20), residues: 679 sheet: -0.94 (0.25), residues: 434 loop : -1.27 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 30 HIS 0.008 0.002 HIS Z 19 PHE 0.024 0.002 PHE S 75 TYR 0.016 0.002 TYR S 38 ARG 0.010 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 194 time to evaluate : 3.022 Fit side-chains REVERT: V 31 TYR cc_start: 0.6080 (p90) cc_final: 0.5786 (p90) REVERT: V 50 MET cc_start: 0.1663 (mtm) cc_final: 0.1443 (mtm) REVERT: D 39 ASP cc_start: 0.7865 (p0) cc_final: 0.7622 (p0) REVERT: D 161 MET cc_start: 0.6691 (mtt) cc_final: 0.6200 (mtp) REVERT: E 116 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: E 153 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7086 (mm) REVERT: E 176 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6992 (p0) REVERT: J 1 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6934 (ptp) REVERT: K 4 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6856 (mm-30) REVERT: K 115 ILE cc_start: 0.6906 (mm) cc_final: 0.6682 (mp) REVERT: S 95 ARG cc_start: 0.5794 (tpt170) cc_final: 0.4396 (ttm170) REVERT: T 1 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6094 (pmm) REVERT: T 32 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8147 (pp) REVERT: O 60 GLU cc_start: 0.7882 (pp20) cc_final: 0.7273 (pm20) REVERT: O 61 GLN cc_start: 0.8146 (pm20) cc_final: 0.7709 (pm20) REVERT: F 96 TRP cc_start: 0.5961 (m100) cc_final: 0.5693 (m100) outliers start: 84 outliers final: 60 residues processed: 250 average time/residue: 0.5906 time to fit residues: 256.6607 Evaluate side-chains 243 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 177 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 79 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 chunk 238 optimal weight: 8.9990 chunk 305 optimal weight: 0.5980 chunk 236 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 416 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 9 GLN P 74 GLN U 52 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 70653 Z= 0.242 Angle : 0.557 8.692 106404 Z= 0.283 Chirality : 0.033 0.227 13716 Planarity : 0.004 0.047 5189 Dihedral : 23.440 176.692 36986 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.28 % Allowed : 17.86 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2135 helix: 0.73 (0.21), residues: 675 sheet: -0.89 (0.25), residues: 441 loop : -1.21 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 30 HIS 0.005 0.001 HIS Z 19 PHE 0.022 0.002 PHE S 75 TYR 0.013 0.002 TYR S 38 ARG 0.009 0.000 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 192 time to evaluate : 2.707 Fit side-chains REVERT: V 31 TYR cc_start: 0.5846 (p90) cc_final: 0.5536 (p90) REVERT: E 153 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6940 (mm) REVERT: E 176 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6928 (p0) REVERT: J 1 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6846 (ptp) REVERT: K 115 ILE cc_start: 0.6860 (mm) cc_final: 0.6644 (mp) REVERT: N 118 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5232 (ttt90) REVERT: S 2 GLU cc_start: 0.7071 (tp30) cc_final: 0.6803 (tp30) REVERT: S 95 ARG cc_start: 0.5795 (tpt170) cc_final: 0.4413 (ttm170) REVERT: T 1 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.5979 (pmm) REVERT: T 32 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8032 (pp) REVERT: O 38 GLN cc_start: 0.7851 (tt0) cc_final: 0.6844 (mp10) REVERT: F 37 MET cc_start: 0.6704 (mtp) cc_final: 0.6376 (mtm) outliers start: 76 outliers final: 55 residues processed: 246 average time/residue: 0.6447 time to fit residues: 273.1356 Evaluate side-chains 238 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 177 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 80 HIS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 79 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 125 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN U 52 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 70653 Z= 0.400 Angle : 0.669 8.609 106404 Z= 0.334 Chirality : 0.038 0.259 13716 Planarity : 0.005 0.057 5189 Dihedral : 23.532 176.849 36986 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.68 % Allowed : 18.08 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.06 (0.18), residues: 2135 helix: 0.52 (0.20), residues: 667 sheet: -0.98 (0.25), residues: 431 loop : -1.37 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 30 HIS 0.008 0.001 HIS Z 19 PHE 0.027 0.002 PHE S 75 TYR 0.017 0.002 TYR Q 24 ARG 0.012 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 188 time to evaluate : 2.713 Fit side-chains revert: symmetry clash REVERT: V 50 MET cc_start: 0.1441 (mtm) cc_final: 0.1170 (mtm) REVERT: D 159 LYS cc_start: 0.6448 (tttp) cc_final: 0.6205 (ttmt) REVERT: D 161 MET cc_start: 0.6704 (mtt) cc_final: 0.6436 (mtp) REVERT: E 153 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7112 (mm) REVERT: E 176 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7007 (p0) REVERT: J 1 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6953 (ptp) REVERT: K 4 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6663 (mm-30) REVERT: K 115 ILE cc_start: 0.6904 (mm) cc_final: 0.6681 (mp) REVERT: N 118 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5418 (ttt90) REVERT: T 1 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6119 (pmm) REVERT: T 32 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8169 (pp) REVERT: O 38 GLN cc_start: 0.7904 (tt0) cc_final: 0.6783 (mp10) outliers start: 83 outliers final: 67 residues processed: 247 average time/residue: 0.6075 time to fit residues: 259.7549 Evaluate side-chains 249 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 176 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 80 HIS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 79 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 1.9990 chunk 398 optimal weight: 30.0000 chunk 363 optimal weight: 2.9990 chunk 388 optimal weight: 30.0000 chunk 233 optimal weight: 0.1980 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 350 optimal weight: 0.9980 chunk 366 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN U 52 ASN 2 16 HIS ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 70653 Z= 0.173 Angle : 0.528 8.945 106404 Z= 0.269 Chirality : 0.031 0.249 13716 Planarity : 0.004 0.047 5189 Dihedral : 23.456 175.778 36986 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.49 % Allowed : 19.32 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 2135 helix: 0.81 (0.20), residues: 673 sheet: -0.77 (0.25), residues: 426 loop : -1.24 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 30 HIS 0.004 0.001 HIS V 88 PHE 0.020 0.001 PHE S 75 TYR 0.014 0.002 TYR V 31 ARG 0.024 0.000 ARG V 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 183 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 50 MET cc_start: 0.1304 (mtm) cc_final: 0.0974 (mtm) REVERT: E 153 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6874 (mm) REVERT: E 176 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6826 (p0) REVERT: K 115 ILE cc_start: 0.6831 (mm) cc_final: 0.6620 (mp) REVERT: N 118 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5367 (ttp80) REVERT: T 1 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.5987 (pmm) REVERT: T 32 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7960 (pp) REVERT: O 38 GLN cc_start: 0.7749 (tt0) cc_final: 0.6801 (mp10) REVERT: F 140 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4050 (tp) outliers start: 62 outliers final: 51 residues processed: 228 average time/residue: 0.6473 time to fit residues: 254.7203 Evaluate side-chains 235 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 178 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 80 HIS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 79 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 3.9990 chunk 410 optimal weight: 30.0000 chunk 250 optimal weight: 1.9990 chunk 194 optimal weight: 50.0000 chunk 285 optimal weight: 20.0000 chunk 430 optimal weight: 5.9990 chunk 396 optimal weight: 40.0000 chunk 342 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN U 52 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 70653 Z= 0.327 Angle : 0.610 8.349 106404 Z= 0.306 Chirality : 0.035 0.272 13716 Planarity : 0.004 0.052 5189 Dihedral : 23.477 177.147 36986 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.61 % Allowed : 19.66 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2135 helix: 0.72 (0.20), residues: 673 sheet: -0.91 (0.25), residues: 433 loop : -1.33 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP P 30 HIS 0.007 0.001 HIS Z 19 PHE 0.024 0.002 PHE S 75 TYR 0.016 0.002 TYR V 31 ARG 0.011 0.001 ARG O 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 182 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 50 MET cc_start: 0.1249 (mtm) cc_final: 0.0951 (mtm) REVERT: V 51 GLN cc_start: 0.4400 (tm-30) cc_final: 0.4054 (tm-30) REVERT: D 161 MET cc_start: 0.6194 (mtt) cc_final: 0.5952 (mtp) REVERT: E 153 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7058 (mm) REVERT: E 176 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.7008 (p0) REVERT: K 66 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7288 (pttm) REVERT: K 115 ILE cc_start: 0.6881 (mm) cc_final: 0.6661 (mp) REVERT: N 118 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.5291 (ttt90) REVERT: T 1 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.5974 (pmm) REVERT: T 32 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8104 (pp) REVERT: O 38 GLN cc_start: 0.7809 (tt0) cc_final: 0.6794 (mp10) outliers start: 64 outliers final: 52 residues processed: 228 average time/residue: 0.6140 time to fit residues: 240.3689 Evaluate side-chains 233 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 175 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 80 HIS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain O residue 19 GLN Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 79 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 50.0000 chunk 365 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.088640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063051 restraints weight = 271687.691| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.57 r_work: 0.3143 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 70653 Z= 0.331 Angle : 0.654 59.193 106404 Z= 0.341 Chirality : 0.036 1.082 13716 Planarity : 0.005 0.061 5189 Dihedral : 23.477 177.148 36986 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.61 % Allowed : 20.23 % Favored : 76.17 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2135 helix: 0.71 (0.20), residues: 673 sheet: -0.91 (0.25), residues: 433 loop : -1.33 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 30 HIS 0.006 0.001 HIS Z 19 PHE 0.024 0.002 PHE S 75 TYR 0.016 0.002 TYR V 31 ARG 0.024 0.001 ARG V 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8223.85 seconds wall clock time: 149 minutes 46.82 seconds (8986.82 seconds total)