Starting phenix.real_space_refine on Sat Feb 24 04:53:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swd_10323/02_2024/6swd_10323_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 1064 5.49 5 Mg 25 5.21 5 S 61 5.16 5 C 22047 2.51 5 N 7689 2.21 5 O 10657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F GLU 219": "OE1" <-> "OE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J GLU 126": "OE1" <-> "OE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 143": "OE1" <-> "OE2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q GLU 83": "OE1" <-> "OE2" Residue "Q GLU 151": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "W GLU 48": "OE1" <-> "OE2" Residue "6 GLU 29": "OE1" <-> "OE2" Residue "6 GLU 42": "OE1" <-> "OE2" Residue "6 GLU 103": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41548 Number of models: 1 Model: "" Number of chains: 28 Chain: "2" Number of atoms: 22543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 22543 Classifications: {'RNA': 1044} Modifications used: {'rna2p': 1, 'rna2p_pur': 77, 'rna2p_pyr': 45, 'rna3p': 30, 'rna3p_pur': 511, 'rna3p_pyr': 379} Link IDs: {'rna2p': 123, 'rna3p': 920} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1533 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "D" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1470 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1983 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 18, 'TRANS': 223} Chain: "F" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "M" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "Q" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1262 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "R" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 900 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "V" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 790 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "W" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "0" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 343 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "5" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 430 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "6" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Unusual residues: {' MG': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25886 SG CYS C 32 65.350 150.459 94.325 1.00 26.53 S ATOM 25907 SG CYS C 35 63.052 152.482 95.695 1.00 35.19 S ATOM 26069 SG CYS C 55 65.678 149.485 97.389 1.00 37.23 S ATOM 26091 SG CYS C 58 61.726 151.071 96.423 1.00 42.19 S ATOM 25745 SG CYS C 14 71.741 137.444 96.265 1.00 22.39 S ATOM 25764 SG CYS C 17 71.556 134.045 98.420 1.00 23.72 S ATOM 25972 SG CYS C 43 73.188 134.115 94.697 1.00 20.55 S ATOM 25994 SG CYS C 46 70.779 133.981 94.859 1.00 20.68 S ATOM 30604 SG CYS F 128 95.448 126.429 114.423 1.00 8.55 S ATOM 30643 SG CYS F 133 98.211 125.450 116.334 1.00 11.68 S ATOM 30660 SG CYS F 135 98.180 128.404 116.099 1.00 13.01 S ATOM 37888 SG CYS R 16 58.699 68.946 146.473 1.00 39.38 S ATOM 37926 SG CYS R 21 62.074 70.021 146.831 1.00 26.42 S ATOM 38414 SG CYS R 77 58.482 70.616 145.034 1.00 32.53 S ATOM 39617 SG CYS W 20 10.102 113.011 94.632 1.00 38.38 S ATOM 39639 SG CYS W 23 7.943 110.695 95.605 1.00 48.30 S ATOM 39765 SG CYS W 39 11.239 109.988 97.806 1.00 41.92 S ATOM 39786 SG CYS W 42 8.868 109.202 95.609 1.00 45.75 S Time building chain proxies: 21.53, per 1000 atoms: 0.52 Number of scatterers: 41548 At special positions: 0 Unit cell: (168.95, 177.67, 207.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 61 16.00 P 1064 15.00 Mg 25 11.99 O 10657 8.00 N 7689 7.00 C 22047 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.70 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 32 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 14 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 46 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 133 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 24 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 21 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 77 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 23 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 20 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 39 " Number of angles added : 24 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 25 sheets defined 22.2% alpha, 16.5% beta 264 base pairs and 583 stacking pairs defined. Time for finding SS restraints: 19.87 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.566A pdb=" N LEU A 16 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 90 through 93 No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 132 through 150 removed outlier: 3.697A pdb=" N ALA A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.542A pdb=" N LEU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 4.456A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 Processing helix chain 'B' and resid 27 through 30 removed outlier: 4.194A pdb=" N LYS B 30 " --> pdb=" O ASP B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 46 through 61 removed outlier: 4.139A pdb=" N VAL B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.657A pdb=" N TYR B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'D' and resid 20 through 33 removed outlier: 3.990A pdb=" N ARG D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 55 removed outlier: 3.652A pdb=" N LYS D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 64 through 79 removed outlier: 3.736A pdb=" N ILE D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 97 through 100 No H-bonds generated for 'chain 'D' and resid 97 through 100' Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.807A pdb=" N ARG D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 49 No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.950A pdb=" N ASN E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'F' and resid 4 through 12 removed outlier: 3.939A pdb=" N TYR F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA F 9 " --> pdb=" O TRP F 5 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS F 10 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 34 through 36 No H-bonds generated for 'chain 'F' and resid 34 through 36' Processing helix chain 'F' and resid 47 through 53 removed outlier: 3.873A pdb=" N ASP F 51 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL F 52 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 53 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 106 through 119 removed outlier: 3.730A pdb=" N LYS F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 177 Processing helix chain 'F' and resid 194 through 209 removed outlier: 4.864A pdb=" N ASN F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 221 removed outlier: 4.437A pdb=" N GLU F 219 " --> pdb=" O PRO F 215 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 220 " --> pdb=" O GLU F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' Processing helix chain 'G' and resid 40 through 43 No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'I' and resid 6 through 17 removed outlier: 3.747A pdb=" N ALA I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 43 removed outlier: 3.683A pdb=" N VAL I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 93 removed outlier: 4.101A pdb=" N ARG I 92 " --> pdb=" O ARG I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 119 removed outlier: 3.922A pdb=" N GLU I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 119 " --> pdb=" O GLU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 89 through 92 No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'M' and resid 53 through 55 No H-bonds generated for 'chain 'M' and resid 53 through 55' Processing helix chain 'M' and resid 57 through 74 removed outlier: 4.019A pdb=" N GLU M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS M 74 " --> pdb=" O GLU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 103 Processing helix chain 'N' and resid 13 through 26 removed outlier: 4.280A pdb=" N TRP N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 34 No H-bonds generated for 'chain 'N' and resid 31 through 34' Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 134 through 139 removed outlier: 3.580A pdb=" N LYS N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 43 removed outlier: 3.556A pdb=" N LEU Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Q 41 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS Q 42 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU Q 43 " --> pdb=" O LYS Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 56 removed outlier: 4.362A pdb=" N GLY Q 51 " --> pdb=" O THR Q 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE Q 53 " --> pdb=" O MET Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 85 removed outlier: 3.941A pdb=" N LYS Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 102 Processing helix chain 'Q' and resid 105 through 108 No H-bonds generated for 'chain 'Q' and resid 105 through 108' Processing helix chain 'Q' and resid 119 through 139 removed outlier: 3.715A pdb=" N GLN Q 123 " --> pdb=" O MET Q 119 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR Q 135 " --> pdb=" O ARG Q 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 43 Processing helix chain 'V' and resid 75 through 81 Processing helix chain 'V' and resid 84 through 89 removed outlier: 3.581A pdb=" N ILE V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) Processing helix chain '0' and resid 16 through 32 removed outlier: 3.796A pdb=" N LYS 0 21 " --> pdb=" O LYS 0 17 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG 0 22 " --> pdb=" O TRP 0 18 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG 0 25 " --> pdb=" O LYS 0 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 0 26 " --> pdb=" O ARG 0 22 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS 0 31 " --> pdb=" O LYS 0 27 " (cutoff:3.500A) Processing helix chain '6' and resid 93 through 96 No H-bonds generated for 'chain '6' and resid 93 through 96' Processing helix chain '6' and resid 102 through 104 No H-bonds generated for 'chain '6' and resid 102 through 104' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.707A pdb=" N GLY A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS A 84 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ARG A 187 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET A 121 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE A 189 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG A 119 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 191 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LYS A 117 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 106 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.961A pdb=" N ARG B 90 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N SER B 71 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 92 " --> pdb=" O SER B 71 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 138 through 141 removed outlier: 6.563A pdb=" N LEU B 152 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE B 154 " --> pdb=" O VAL B 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.925A pdb=" N VAL B 42 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 28 through 31 Processing sheet with id= G, first strand: chain 'D' and resid 130 through 132 removed outlier: 3.638A pdb=" N THR D 153 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 101 through 104 removed outlier: 3.829A pdb=" N LEU E 103 " --> pdb=" O ILE E 111 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 122 through 126 Processing sheet with id= J, first strand: chain 'E' and resid 147 through 150 Processing sheet with id= K, first strand: chain 'E' and resid 230 through 232 removed outlier: 6.603A pdb=" N THR E 214 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE E 202 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL E 212 " --> pdb=" O ILE E 202 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.606A pdb=" N ASP F 67 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 145 through 149 Processing sheet with id= N, first strand: chain 'G' and resid 15 through 22 removed outlier: 3.910A pdb=" N ILE G 15 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY G 65 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS G 122 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE G 63 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL G 124 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N MET G 61 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 83 through 88 Processing sheet with id= P, first strand: chain 'I' and resid 24 through 27 Processing sheet with id= Q, first strand: chain 'I' and resid 71 through 74 removed outlier: 3.814A pdb=" N LYS I 71 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG I 124 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR I 128 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE I 101 " --> pdb=" O TYR I 128 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 43 through 47 Processing sheet with id= S, first strand: chain 'M' and resid 38 through 43 removed outlier: 6.733A pdb=" N ILE M 30 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG M 41 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE M 28 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER M 43 " --> pdb=" O THR M 26 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR M 26 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY M 78 " --> pdb=" O GLY M 15 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA M 17 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS M 80 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE M 19 " --> pdb=" O HIS M 80 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG M 82 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER M 21 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG M 84 " --> pdb=" O SER M 21 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'N' and resid 83 through 87 removed outlier: 4.010A pdb=" N LYS N 128 " --> pdb=" O ILE N 104 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU N 106 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL N 126 " --> pdb=" O GLU N 106 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 57 through 61 Processing sheet with id= V, first strand: chain 'R' and resid 63 through 73 removed outlier: 3.855A pdb=" N SER R 40 " --> pdb=" O THR R 48 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU R 50 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL R 38 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLN R 52 " --> pdb=" O GLY R 36 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N GLY R 36 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 15.597A pdb=" N TYR R 54 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 16.853A pdb=" N PHE R 34 " --> pdb=" O TYR R 54 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 88 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA R 104 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA R 89 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL R 102 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'V' and resid 2 through 11 removed outlier: 6.424A pdb=" N TYR V 20 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL V 8 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU V 18 " --> pdb=" O VAL V 8 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU V 10 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG V 16 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE V 21 " --> pdb=" O GLY V 67 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY V 67 " --> pdb=" O PHE V 21 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS V 70 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE V 53 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR V 72 " --> pdb=" O THR V 51 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR V 51 " --> pdb=" O TYR V 72 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '6' and resid 23 through 27 removed outlier: 3.780A pdb=" N TYR 6 84 " --> pdb=" O ILE 6 68 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN 6 70 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE 6 82 " --> pdb=" O GLN 6 70 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '6' and resid 37 through 40 390 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 715 hydrogen bonds 1256 hydrogen bond angles 0 basepair planarities 264 basepair parallelities 583 stacking parallelities Total time for adding SS restraints: 25.52 Time building geometry restraints manager: 19.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4038 1.28 - 1.42: 17237 1.42 - 1.55: 21069 1.55 - 1.68: 2129 1.68 - 1.81: 101 Bond restraints: 44574 Sorted by residual: bond pdb=" C2' A2M 2 373 " pdb=" C1' A2M 2 373 " ideal model delta sigma weight residual 1.305 1.504 -0.199 2.00e-02 2.50e+03 9.95e+01 bond pdb=" O4' A2M 2 373 " pdb=" C1' A2M 2 373 " ideal model delta sigma weight residual 1.615 1.418 0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" C5 4AC 2 703 " pdb=" C6 4AC 2 703 " ideal model delta sigma weight residual 1.493 1.302 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" N3 4AC 2 851 " pdb=" C4 4AC 2 851 " ideal model delta sigma weight residual 1.449 1.262 0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" N1 LHH 2 250 " pdb=" C2 LHH 2 250 " ideal model delta sigma weight residual 1.503 1.318 0.185 2.00e-02 2.50e+03 8.53e+01 ... (remaining 44569 not shown) Histogram of bond angle deviations from ideal: 97.47 - 105.40: 5666 105.40 - 113.32: 26496 113.32 - 121.25: 21407 121.25 - 129.18: 10813 129.18 - 137.10: 1077 Bond angle restraints: 65459 Sorted by residual: angle pdb=" C1' A2M 2 373 " pdb=" N9 A2M 2 373 " pdb=" C8 A2M 2 373 " ideal model delta sigma weight residual 88.50 123.12 -34.62 3.00e+00 1.11e-01 1.33e+02 angle pdb=" N6 A2M 2 373 " pdb=" C6 A2M 2 373 " pdb=" N1 A2M 2 373 " ideal model delta sigma weight residual 92.14 121.37 -29.23 3.00e+00 1.11e-01 9.49e+01 angle pdb=" C CYS 6 41 " pdb=" N GLU 6 42 " pdb=" CA GLU 6 42 " ideal model delta sigma weight residual 122.73 114.96 7.77 1.61e+00 3.86e-01 2.33e+01 angle pdb=" N VAL W 63 " pdb=" CA VAL W 63 " pdb=" C VAL W 63 " ideal model delta sigma weight residual 113.47 108.73 4.74 1.01e+00 9.80e-01 2.20e+01 angle pdb=" N6 MA6 21488 " pdb=" C6 MA6 21488 " pdb=" N1 MA6 21488 " ideal model delta sigma weight residual 104.44 118.46 -14.02 3.00e+00 1.11e-01 2.18e+01 ... (remaining 65454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 25445 34.50 - 68.99: 2756 68.99 - 103.49: 329 103.49 - 137.99: 3 137.99 - 172.48: 1 Dihedral angle restraints: 28534 sinusoidal: 21955 harmonic: 6579 Sorted by residual: dihedral pdb=" O4' C 2 721 " pdb=" C1' C 2 721 " pdb=" N1 C 2 721 " pdb=" C2 C 2 721 " ideal model delta sinusoidal sigma weight residual 200.00 75.80 124.20 1 1.50e+01 4.44e-03 6.66e+01 dihedral pdb=" O4' C 21498 " pdb=" C1' C 21498 " pdb=" N1 C 21498 " pdb=" C2 C 21498 " ideal model delta sinusoidal sigma weight residual -128.00 44.48 -172.48 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA LYS N 5 " pdb=" C LYS N 5 " pdb=" N ALA N 6 " pdb=" CA ALA N 6 " ideal model delta harmonic sigma weight residual -180.00 -148.78 -31.22 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 28531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 5646 0.054 - 0.108: 1901 0.108 - 0.162: 406 0.162 - 0.216: 70 0.216 - 0.270: 16 Chirality restraints: 8039 Sorted by residual: chirality pdb=" C1' A 2 529 " pdb=" O4' A 2 529 " pdb=" C2' A 2 529 " pdb=" N9 A 2 529 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1' A 2 759 " pdb=" O4' A 2 759 " pdb=" C2' A 2 759 " pdb=" N9 A 2 759 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1' C 2 721 " pdb=" O4' C 2 721 " pdb=" C2' C 2 721 " pdb=" N1 C 2 721 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 8036 not shown) Planarity restraints: 4312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 21376 " 0.008 2.00e-02 2.50e+03 5.51e-01 6.82e+03 pdb=" C4' OMC 21376 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMC 21376 " 0.642 2.00e-02 2.50e+03 pdb=" C3' OMC 21376 " -0.575 2.00e-02 2.50e+03 pdb=" O3' OMC 21376 " -0.511 2.00e-02 2.50e+03 pdb=" C2' OMC 21376 " -0.234 2.00e-02 2.50e+03 pdb=" O2' OMC 21376 " 0.852 2.00e-02 2.50e+03 pdb=" C1' OMC 21376 " 0.226 2.00e-02 2.50e+03 pdb=" N1 OMC 21376 " -0.840 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 59 " 0.044 2.00e-02 2.50e+03 1.97e-02 1.07e+01 pdb=" N9 A 2 59 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A 2 59 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 2 59 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 2 59 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 2 59 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A 2 59 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A 2 59 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A 2 59 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A 2 59 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A 2 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 587 " 0.041 2.00e-02 2.50e+03 1.86e-02 9.52e+00 pdb=" N9 A 2 587 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A 2 587 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A 2 587 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A 2 587 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A 2 587 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A 2 587 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A 2 587 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A 2 587 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A 2 587 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A 2 587 " -0.005 2.00e-02 2.50e+03 ... (remaining 4309 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 112 2.45 - 3.06: 23606 3.06 - 3.67: 62795 3.67 - 4.29: 105475 4.29 - 4.90: 156307 Nonbonded interactions: 348295 Sorted by model distance: nonbonded pdb=" OP2 G 2 727 " pdb="MG MG 21608 " model vdw 1.835 2.170 nonbonded pdb=" OP2 G 2 113 " pdb="MG MG 21622 " model vdw 1.960 2.170 nonbonded pdb=" OP1 A 2 587 " pdb="MG MG 21606 " model vdw 2.003 2.170 nonbonded pdb=" OP1 G 21474 " pdb="MG MG 21609 " model vdw 2.030 2.170 nonbonded pdb=" O TYR A 23 " pdb=" OG1 THR A 81 " model vdw 2.069 2.440 ... (remaining 348290 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: 2.630 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: 0.020 Extract box with map and model: 11.090 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 133.190 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.150 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.199 44574 Z= 0.886 Angle : 1.069 34.616 65459 Z= 0.528 Chirality : 0.056 0.270 8039 Planarity : 0.011 0.551 4312 Dihedral : 22.507 172.482 24310 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.62 % Favored : 89.29 % Rotamer: Outliers : 1.12 % Allowed : 11.79 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.14), residues: 2259 helix: -3.45 (0.16), residues: 516 sheet: -2.65 (0.22), residues: 460 loop : -3.37 (0.14), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP 6 60 HIS 0.015 0.003 HIS I 13 PHE 0.054 0.004 PHE F 197 TYR 0.026 0.003 TYR I 130 ARG 0.010 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 390 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 217 ASP cc_start: 0.7571 (p0) cc_final: 0.7366 (p0) REVERT: E 224 ASP cc_start: 0.6292 (p0) cc_final: 0.6078 (p0) REVERT: N 76 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: W 22 ASP cc_start: 0.7085 (p0) cc_final: 0.6873 (p0) outliers start: 22 outliers final: 8 residues processed: 406 average time/residue: 0.5801 time to fit residues: 374.7593 Evaluate side-chains 306 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 297 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain N residue 76 GLN Chi-restraints excluded: chain 6 residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 255 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 65 GLN C 34 ASN D 176 GLN E 99 HIS E 192 ASN F 35 HIS I 9 ASN M 18 HIS M 80 HIS N 8 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 ASN Q 85 HIS Q 112 HIS W 27 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44574 Z= 0.175 Angle : 0.619 15.541 65459 Z= 0.318 Chirality : 0.038 0.215 8039 Planarity : 0.005 0.108 4312 Dihedral : 22.896 172.807 19426 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.03 % Allowed : 15.80 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.16), residues: 2259 helix: -1.86 (0.22), residues: 489 sheet: -1.91 (0.23), residues: 465 loop : -2.69 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 0 18 HIS 0.005 0.001 HIS Q 5 PHE 0.014 0.001 PHE F 197 TYR 0.016 0.001 TYR Q 148 ARG 0.006 0.000 ARG 6 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 356 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 224 ASP cc_start: 0.6281 (p0) cc_final: 0.5908 (p0) REVERT: I 61 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: M 46 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6520 (mtp) REVERT: N 61 GLU cc_start: 0.6523 (tp30) cc_final: 0.6260 (tp30) REVERT: Q 149 ASP cc_start: 0.6091 (p0) cc_final: 0.5804 (p0) REVERT: R 94 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8043 (mm) outliers start: 40 outliers final: 22 residues processed: 376 average time/residue: 0.5236 time to fit residues: 326.0483 Evaluate side-chains 335 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 310 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 203 ASN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN N 66 ASN Q 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 44574 Z= 0.362 Angle : 0.650 16.010 65459 Z= 0.331 Chirality : 0.039 0.220 8039 Planarity : 0.005 0.120 4312 Dihedral : 22.799 169.042 19418 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.17 % Allowed : 16.46 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.17), residues: 2259 helix: -1.20 (0.23), residues: 505 sheet: -1.49 (0.23), residues: 458 loop : -2.36 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 0 18 HIS 0.004 0.001 HIS F 139 PHE 0.023 0.002 PHE F 197 TYR 0.014 0.001 TYR J 62 ARG 0.008 0.001 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 312 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 MET cc_start: 0.7512 (tmm) cc_final: 0.7257 (tmm) REVERT: E 224 ASP cc_start: 0.6478 (p0) cc_final: 0.6017 (p0) REVERT: I 61 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: R 94 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8138 (mm) outliers start: 82 outliers final: 55 residues processed: 362 average time/residue: 0.5210 time to fit residues: 317.4116 Evaluate side-chains 355 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 298 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 0 residue 26 LEU Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 141 optimal weight: 0.2980 chunk 199 optimal weight: 0.3980 chunk 297 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN Q 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 44574 Z= 0.202 Angle : 0.570 15.799 65459 Z= 0.291 Chirality : 0.036 0.223 8039 Planarity : 0.004 0.115 4312 Dihedral : 22.743 171.449 19418 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.46 % Allowed : 17.68 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2259 helix: -0.68 (0.24), residues: 503 sheet: -1.25 (0.24), residues: 458 loop : -2.01 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 0 18 HIS 0.004 0.001 HIS Q 5 PHE 0.012 0.001 PHE F 197 TYR 0.011 0.001 TYR B 177 ARG 0.005 0.000 ARG W 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 328 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 VAL cc_start: 0.7630 (t) cc_final: 0.7378 (t) REVERT: E 224 ASP cc_start: 0.6296 (p0) cc_final: 0.5878 (p0) REVERT: I 61 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: R 94 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8130 (mm) outliers start: 68 outliers final: 45 residues processed: 368 average time/residue: 0.5516 time to fit residues: 343.6070 Evaluate side-chains 358 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 311 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 37 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN Q 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 44574 Z= 0.341 Angle : 0.625 15.665 65459 Z= 0.317 Chirality : 0.039 0.224 8039 Planarity : 0.005 0.117 4312 Dihedral : 22.701 169.787 19418 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.17 % Allowed : 19.05 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2259 helix: -0.54 (0.23), residues: 521 sheet: -1.14 (0.24), residues: 453 loop : -1.92 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 0 18 HIS 0.004 0.001 HIS F 139 PHE 0.015 0.001 PHE E 186 TYR 0.018 0.001 TYR B 177 ARG 0.007 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 306 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8403 (ptm-80) REVERT: E 168 VAL cc_start: 0.7745 (t) cc_final: 0.7493 (t) REVERT: E 224 ASP cc_start: 0.6402 (p0) cc_final: 0.5933 (p0) REVERT: I 61 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: R 94 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8209 (mm) REVERT: V 1 MET cc_start: 0.8126 (ppp) cc_final: 0.7839 (ppp) outliers start: 82 outliers final: 62 residues processed: 359 average time/residue: 0.5065 time to fit residues: 305.5050 Evaluate side-chains 360 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 295 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 315 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 146 optimal weight: 0.0370 chunk 26 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 37 GLN B 178 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44574 Z= 0.236 Angle : 0.581 15.789 65459 Z= 0.296 Chirality : 0.036 0.226 8039 Planarity : 0.004 0.115 4312 Dihedral : 22.689 170.954 19418 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.81 % Allowed : 19.87 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 2259 helix: -0.23 (0.24), residues: 514 sheet: -1.03 (0.24), residues: 462 loop : -1.77 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 0 18 HIS 0.004 0.001 HIS W 32 PHE 0.013 0.001 PHE E 186 TYR 0.015 0.001 TYR B 177 ARG 0.004 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 311 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8472 (ptm-80) REVERT: E 168 VAL cc_start: 0.7751 (t) cc_final: 0.7489 (t) REVERT: E 207 MET cc_start: 0.7162 (tpp) cc_final: 0.6882 (tpp) REVERT: E 224 ASP cc_start: 0.6321 (p0) cc_final: 0.5859 (p0) REVERT: I 61 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: N 98 ASP cc_start: 0.7177 (m-30) cc_final: 0.6761 (m-30) REVERT: R 94 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8134 (mm) outliers start: 75 outliers final: 57 residues processed: 361 average time/residue: 0.5026 time to fit residues: 305.2875 Evaluate side-chains 361 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 301 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 314 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 145 optimal weight: 0.0030 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 37 GLN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN Q 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44574 Z= 0.177 Angle : 0.557 15.694 65459 Z= 0.282 Chirality : 0.035 0.220 8039 Planarity : 0.004 0.115 4312 Dihedral : 22.663 172.817 19418 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.51 % Allowed : 20.02 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2259 helix: 0.13 (0.24), residues: 513 sheet: -0.87 (0.24), residues: 458 loop : -1.66 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 25 HIS 0.003 0.001 HIS Q 5 PHE 0.011 0.001 PHE E 186 TYR 0.017 0.001 TYR B 177 ARG 0.008 0.000 ARG W 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 320 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 VAL cc_start: 0.7750 (t) cc_final: 0.7509 (t) REVERT: E 207 MET cc_start: 0.7173 (tpp) cc_final: 0.6912 (tpp) REVERT: E 224 ASP cc_start: 0.6239 (p0) cc_final: 0.5796 (p0) REVERT: I 61 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: R 94 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8071 (mm) outliers start: 69 outliers final: 55 residues processed: 365 average time/residue: 0.5133 time to fit residues: 315.2793 Evaluate side-chains 365 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 308 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 119 MET Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 83 VAL Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 44574 Z= 0.323 Angle : 0.615 15.878 65459 Z= 0.311 Chirality : 0.038 0.222 8039 Planarity : 0.005 0.116 4312 Dihedral : 22.628 170.732 19416 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.61 % Allowed : 20.43 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 2259 helix: 0.18 (0.24), residues: 515 sheet: -0.84 (0.24), residues: 455 loop : -1.64 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 60 HIS 0.003 0.001 HIS F 139 PHE 0.017 0.001 PHE E 186 TYR 0.017 0.001 TYR B 177 ARG 0.006 0.000 ARG W 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 304 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 VAL cc_start: 0.7787 (t) cc_final: 0.7530 (t) REVERT: E 207 MET cc_start: 0.7184 (tpp) cc_final: 0.6787 (tpp) REVERT: E 224 ASP cc_start: 0.6384 (p0) cc_final: 0.5942 (p0) REVERT: I 61 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: Q 93 GLU cc_start: 0.5720 (tp30) cc_final: 0.4889 (tp30) REVERT: R 94 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8200 (mm) outliers start: 71 outliers final: 61 residues processed: 352 average time/residue: 0.4987 time to fit residues: 296.6822 Evaluate side-chains 361 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 298 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 0 residue 26 LEU Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 68 ILE Chi-restraints excluded: chain 6 residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 chunk 274 optimal weight: 0.0050 chunk 292 optimal weight: 0.6980 chunk 300 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 89 optimal weight: 40.0000 chunk 264 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 37 GLN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 44574 Z= 0.129 Angle : 0.548 15.756 65459 Z= 0.277 Chirality : 0.034 0.248 8039 Planarity : 0.004 0.113 4312 Dihedral : 22.651 174.312 19416 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.44 % Allowed : 21.60 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2259 helix: 0.50 (0.24), residues: 513 sheet: -0.65 (0.25), residues: 456 loop : -1.51 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 41 HIS 0.003 0.001 HIS Q 5 PHE 0.007 0.001 PHE I 79 TYR 0.015 0.001 TYR B 177 ARG 0.006 0.000 ARG W 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 326 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 VAL cc_start: 0.7726 (t) cc_final: 0.7486 (t) REVERT: E 224 ASP cc_start: 0.6257 (p0) cc_final: 0.5855 (p0) REVERT: I 61 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: R 94 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8059 (mm) REVERT: 6 96 ARG cc_start: 0.6855 (ttm170) cc_final: 0.6642 (pmt-80) outliers start: 48 outliers final: 41 residues processed: 359 average time/residue: 0.5012 time to fit residues: 301.8253 Evaluate side-chains 354 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 311 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 7.9990 chunk 192 optimal weight: 0.0060 chunk 309 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 298 optimal weight: 0.7980 chunk 258 optimal weight: 0.1980 chunk 26 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 44574 Z= 0.253 Angle : 0.586 15.763 65459 Z= 0.295 Chirality : 0.036 0.264 8039 Planarity : 0.005 0.115 4312 Dihedral : 22.600 172.453 19416 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.85 % Allowed : 21.90 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2259 helix: 0.58 (0.24), residues: 510 sheet: -0.67 (0.24), residues: 459 loop : -1.47 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 0 18 HIS 0.003 0.001 HIS F 139 PHE 0.015 0.001 PHE E 186 TYR 0.016 0.001 TYR B 177 ARG 0.014 0.000 ARG W 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4518 Ramachandran restraints generated. 2259 Oldfield, 0 Emsley, 2259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 305 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 VAL cc_start: 0.7752 (t) cc_final: 0.7535 (t) REVERT: E 224 ASP cc_start: 0.6257 (p0) cc_final: 0.5935 (p0) REVERT: I 61 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: R 94 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8155 (mm) outliers start: 56 outliers final: 50 residues processed: 343 average time/residue: 0.5187 time to fit residues: 298.3176 Evaluate side-chains 355 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 303 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 259 optimal weight: 0.9990 chunk 108 optimal weight: 0.0570 chunk 265 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.045093 restraints weight = 159138.762| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.73 r_work: 0.2531 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 44574 Z= 0.152 Angle : 0.558 15.752 65459 Z= 0.281 Chirality : 0.034 0.246 8039 Planarity : 0.004 0.114 4312 Dihedral : 22.628 173.437 19416 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.24 % Allowed : 22.31 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2259 helix: 0.65 (0.25), residues: 510 sheet: -0.54 (0.25), residues: 458 loop : -1.42 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 41 HIS 0.003 0.001 HIS Q 5 PHE 0.011 0.001 PHE E 186 TYR 0.017 0.001 TYR B 177 ARG 0.006 0.000 ARG G 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7833.11 seconds wall clock time: 143 minutes 23.04 seconds (8603.04 seconds total)